diff --git a/.travis.yml b/.travis.yml index 1bd018f3..4fd7b149 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,6 +11,7 @@ dist: xenial python: - "3.6" - "3.7" + - "3.8" install: - pip install -U pip setuptools wheel tox-travis coveralls diff --git a/allel/opt/io_vcf_read.c b/allel/opt/io_vcf_read.c index 76d325da..5a50b4c9 100644 --- a/allel/opt/io_vcf_read.c +++ b/allel/opt/io_vcf_read.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.29.10 */ +/* Generated by Cython 0.29.20 */ /* BEGIN: Cython Metadata { @@ -20,8 +20,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_10" -#define CYTHON_HEX_VERSION 0x001D0AF0 +#define CYTHON_ABI "0_29_20" +#define CYTHON_HEX_VERSION 0x001D14F0 #define CYTHON_FUTURE_DIVISION 1 #include #ifndef offsetof @@ -323,12 +323,12 @@ END: Cython Metadata */ #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" -#if PY_VERSION_HEX < 0x030800A4 +#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2 #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #define __Pyx_DefaultClassType PyType_Type #endif @@ -497,8 +497,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact +#ifndef PyObject_Unicode #define PyObject_Unicode PyObject_Str #endif +#endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) @@ -509,6 +511,13 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif +#if PY_VERSION_HEX >= 0x030900A4 + #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) +#else + #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) +#endif #if CYTHON_ASSUME_SAFE_MACROS #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) #else @@ -589,11 +598,10 @@ static CYTHON_INLINE float __PYX_NAN() { #define __Pyx_truncl truncl #endif - +#define __PYX_MARK_ERR_POS(f_index, lineno) \ + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } #define __PYX_ERR(f_index, lineno, Ln_error) \ -{ \ - __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ -} + { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } #ifndef __PYX_EXTERN_C #ifdef __cplusplus @@ -611,6 +619,9 @@ static CYTHON_INLINE float __PYX_NAN() { #include #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" + + /* NumPy API declarations from "numpy/__init__.pxd" */ + #include "pythread.h" #include "pystate.h" #ifdef _OPENMP @@ -957,7 +968,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":697 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -966,7 +977,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":698 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -975,7 +986,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":699 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -984,7 +995,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":700 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -993,7 +1004,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":704 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1002,7 +1013,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":705 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1011,7 +1022,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":706 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1020,7 +1031,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":707 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1029,7 +1040,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":711 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1038,7 +1049,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":712 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1047,7 +1058,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":721 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1056,7 +1067,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":722 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1065,7 +1076,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":723 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1074,7 +1085,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":725 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1083,7 +1094,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":726 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1092,7 +1103,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":727 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1101,7 +1112,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":729 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1110,7 +1121,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":730 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1119,7 +1130,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":732 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1128,7 +1139,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":733 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1137,7 +1148,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":734 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1243,7 +1254,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":736 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1252,7 +1263,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":737 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1261,7 +1272,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":738 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1270,7 +1281,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":740 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -2623,7 +2634,7 @@ struct __pyx_memoryview_obj { }; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -3585,7 +3596,7 @@ struct __pyx_vtabstruct_memoryview { static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -3800,7 +3811,7 @@ static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObje #define __Pyx_PyFunction_FastCall(func, args, nargs)\ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); #else #define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) #endif @@ -3873,7 +3884,7 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -4210,7 +4221,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -4248,6 +4259,9 @@ static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_nam /* SetVTable.proto */ static int __Pyx_SetVtable(PyObject *dict, void *vtable); +/* PyObjectGetAttrStrNoError.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); + /* SetupReduce.proto */ static int __Pyx_setup_reduce(PyObject* type_obj); @@ -5490,7 +5504,6 @@ static const char __pyx_k_pyx_unpickle_VCFQualParser[] = "__pyx_unpickle_VCFQual static const char __pyx_k_ANN_ANNOTATION_IMPACT_FIELD[] = "ANN_ANNOTATION_IMPACT_FIELD"; static const char __pyx_k_error_parsing_integer_value[] = "error parsing integer value"; static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static const char __pyx_k_pyx_unpickle_ANNTransformer[] = "__pyx_unpickle_ANNTransformer"; static const char __pyx_k_ANN_TRANSCRIPT_BIOTYPE_FIELD[] = "ANN_TRANSCRIPT_BIOTYPE_FIELD"; static const char __pyx_k_not_supported_for_INFO_field[] = " not supported for INFO field "; @@ -5592,7 +5605,6 @@ static const char __pyx_k_expected_string_S_or_object_O_dt[] = "expected string static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; static const char __pyx_k_invalid_ANN_field_r_will_be_igno[] = "invalid ANN field %r, will be ignored"; static const char __pyx_k_more_samples_than_given_in_heade[] = "more samples than given in header"; -static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; static const char __pyx_k_not_all_characters_parsed_for_fl[] = "not all characters parsed for floating point value"; static const char __pyx_k_not_all_characters_parsed_for_in[] = "not all characters parsed for integer value"; @@ -5895,8 +5907,6 @@ static PyObject *__pyx_n_s_n_samples_out; static PyObject *__pyx_n_s_name; static PyObject *__pyx_n_s_name_2; static PyObject *__pyx_n_s_nan; -static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; -static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_ndim; static PyObject *__pyx_n_s_new; static PyObject *__pyx_n_s_newaxis; @@ -6392,8 +6402,6 @@ static PyObject *__pyx_pf_5allel_3opt_11io_vcf_read_124__pyx_unpickle_VCFCallDat static PyObject *__pyx_pf_5allel_3opt_11io_vcf_read_126__pyx_unpickle_VCFCallDataStringParser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5allel_3opt_11io_vcf_read_128__pyx_unpickle_VCFCallDataObjectParser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5allel_3opt_11io_vcf_read_130__pyx_unpickle_ANNTransformer(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); 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+ + /* "View.MemoryView":378 + * + * (<__pyx_buffer *> &self.view).obj = NULL + * Py_DECREF(Py_None) # <<<<<<<<<<<<<< + * + * cdef int i + */ + Py_DECREF(Py_None); + + /* "View.MemoryView":375 + * if self.obj is not None: + * __Pyx_ReleaseBuffer(&self.view) + * elif (<__pyx_buffer *> &self.view).obj == Py_None: # <<<<<<<<<<<<<< + * + * (<__pyx_buffer *> &self.view).obj = NULL */ } + __pyx_L3:; - /* "View.MemoryView":378 + /* "View.MemoryView":382 * cdef int i * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: # <<<<<<<<<<<<<< @@ -123071,7 +124305,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_self->lock != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":379 + /* "View.MemoryView":383 * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): # <<<<<<<<<<<<<< @@ -123083,7 +124317,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -123093,7 +124327,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = (((__pyx_memoryview_thread_locks[__pyx_v_i]) == __pyx_v_self->lock) != 0); if (__pyx_t_2) { - /* "View.MemoryView":381 + /* "View.MemoryView":385 * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 # <<<<<<<<<<<<<< @@ -123102,7 +124336,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ __pyx_memoryview_thread_locks_used = (__pyx_memoryview_thread_locks_used - 1); - /* "View.MemoryView":382 + /* "View.MemoryView":386 * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: # <<<<<<<<<<<<<< @@ -123112,7 +124346,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_i != __pyx_memoryview_thread_locks_used) != 0); if (__pyx_t_2) { - /* "View.MemoryView":384 + /* "View.MemoryView":388 * if i != __pyx_memoryview_thread_locks_used: * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( * __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i]) # <<<<<<<<<<<<<< @@ -123122,7 +124356,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_6 = (__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]); __pyx_t_7 = (__pyx_memoryview_thread_locks[__pyx_v_i]); - /* "View.MemoryView":383 + /* "View.MemoryView":387 * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( # <<<<<<<<<<<<<< @@ -123132,7 +124366,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal (__pyx_memoryview_thread_locks[__pyx_v_i]) = __pyx_t_6; (__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]) = __pyx_t_7; - /* "View.MemoryView":382 + /* "View.MemoryView":386 * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: # <<<<<<<<<<<<<< @@ -123141,7 +124375,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ } - /* "View.MemoryView":385 + /* "View.MemoryView":389 * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( * __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i]) * break # <<<<<<<<<<<<<< @@ -123150,7 +124384,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ goto __pyx_L6_break; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -123161,7 +124395,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } /*else*/ { - /* "View.MemoryView":387 + /* "View.MemoryView":391 * break * else: * PyThread_free_lock(self.lock) # <<<<<<<<<<<<<< @@ -123172,7 +124406,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } __pyx_L6_break:; 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__Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 393, __pyx_L1_error) + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 397, __pyx_L1_error) #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 393, __pyx_L1_error) + __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 397, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } else { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 393, __pyx_L1_error) + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 397, __pyx_L1_error) #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); 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__pyx_v_info->shape = __pyx_t_4; - /* "View.MemoryView":518 + /* "View.MemoryView":522 * raise ValueError("Cannot create writable memory view from read-only memoryview") * * if flags & PyBUF_ND: # <<<<<<<<<<<<<< @@ -124992,7 +126262,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu goto __pyx_L6; } - /* "View.MemoryView":521 + /* "View.MemoryView":525 * info.shape = self.view.shape * else: * info.shape = NULL # <<<<<<<<<<<<<< @@ -125004,7 +126274,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu } __pyx_L6:; - /* "View.MemoryView":523 + /* "View.MemoryView":527 * info.shape = NULL * * if flags & PyBUF_STRIDES: # <<<<<<<<<<<<<< @@ -125014,7 +126284,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_STRIDES) != 0); if (__pyx_t_1) { - /* "View.MemoryView":524 + /* "View.MemoryView":528 * * if flags & PyBUF_STRIDES: * info.strides = self.view.strides # <<<<<<<<<<<<<< @@ -125024,7 +126294,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_4 = __pyx_v_self->view.strides; 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- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(1, 758, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(1, 762, __pyx_L1_error) if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(1, 758, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(1, 762, __pyx_L1_error) __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L11_bool_binop_done; @@ -127736,55 +129070,55 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L11_bool_binop_done:; __pyx_v_step = __pyx_t_10; - /* "View.MemoryView":760 + /* "View.MemoryView":764 * step = index.step or 0 * * have_start = index.start is not None # <<<<<<<<<<<<<< * have_stop = index.stop is not None * have_step = index.step is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 760, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 764, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_start = __pyx_t_1; - /* "View.MemoryView":761 + /* "View.MemoryView":765 * * have_start = index.start is not None * have_stop = index.stop is not None # <<<<<<<<<<<<<< * have_step = index.step is not None * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 761, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 765, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_stop = __pyx_t_1; - /* "View.MemoryView":762 + /* "View.MemoryView":766 * have_start = index.start is not None * have_stop = index.stop is not None * have_step = index.step is not None # <<<<<<<<<<<<<< * * slice_memviewslice( */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 762, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 766, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_step = __pyx_t_1; - /* "View.MemoryView":764 + /* "View.MemoryView":768 * have_step = index.step is not None * * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(1, 764, __pyx_L1_error) + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(1, 768, __pyx_L1_error) - /* "View.MemoryView":770 + /* "View.MemoryView":774 * have_start, have_stop, have_step, * True) * new_ndim += 1 # <<<<<<<<<<<<<< @@ -127795,7 +129129,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L6:; - /* "View.MemoryView":742 + /* "View.MemoryView":746 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -127805,7 +129139,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -127816,7 +129150,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< @@ -127825,39 +129159,39 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":774 + /* "View.MemoryView":778 * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, # <<<<<<<<<<<<<< * memviewsliceobj.to_dtype_func, * memview.dtype_is_object) */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(1, 774, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(1, 778, __pyx_L1_error) } - /* "View.MemoryView":775 + /* "View.MemoryView":779 * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, # <<<<<<<<<<<<<< * memview.dtype_is_object) * else: */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(1, 775, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(1, 779, __pyx_L1_error) } - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 773, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 777, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(1, 773, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(1, 777, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -127866,7 +129200,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ } - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< @@ -127876,30 +129210,30 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ /*else*/ { __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":779 + /* "View.MemoryView":783 * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 778, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 782, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(1, 778, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(1, 782, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":706 + /* "View.MemoryView":710 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -127921,7 +129255,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ return __pyx_r; } -/* "View.MemoryView":803 +/* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -127936,8 +129270,11 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, int __pyx_t_1; int __pyx_t_2; int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -127947,7 +129284,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -127957,7 +129294,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((__pyx_v_start < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":826 + /* "View.MemoryView":830 * * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -127966,7 +129303,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -127975,7 +129312,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -127989,16 +129326,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":828 + /* "View.MemoryView":832 * start += shape * if not 0 <= start < shape: * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< * else: * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 828, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 832, __pyx_L1_error) - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -128007,7 +129344,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -128017,7 +129354,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L3; } - /* "View.MemoryView":831 + /* "View.MemoryView":835 * else: * * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< @@ -128036,7 +129373,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L6_bool_binop_done:; __pyx_v_negative_step = __pyx_t_2; - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -128054,16 +129391,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L9_bool_binop_done:; if (__pyx_t_2) { - /* "View.MemoryView":834 + /* "View.MemoryView":838 * * if have_step and step == 0: * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 834, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 838, __pyx_L1_error) - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -128072,7 +129409,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -128082,7 +129419,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_start != 0); if (__pyx_t_2) { - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -128092,7 +129429,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":839 + /* "View.MemoryView":843 * if have_start: * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -128101,7 +129438,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -128111,7 +129448,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":841 + /* "View.MemoryView":845 * start += shape * if start < 0: * start = 0 # <<<<<<<<<<<<<< @@ -128120,7 +129457,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = 0; - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -128129,7 +129466,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -128139,7 +129476,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L12; } - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -128149,7 +129486,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -128159,7 +129496,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":844 + /* "View.MemoryView":848 * elif start >= shape: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -128168,7 +129505,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -128178,7 +129515,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L14; } - /* "View.MemoryView":846 + /* "View.MemoryView":850 * start = shape - 1 * else: * start = shape # <<<<<<<<<<<<<< @@ -128190,7 +129527,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L14:; - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -128200,7 +129537,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L12:; - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -128210,7 +129547,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L11; } - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -128221,7 +129558,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":849 + /* "View.MemoryView":853 * else: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -128230,7 +129567,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -128240,7 +129577,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L15; } - /* "View.MemoryView":851 + /* "View.MemoryView":855 * start = shape - 1 * else: * start = 0 # <<<<<<<<<<<<<< @@ -128254,7 +129591,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L11:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -128264,7 +129601,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_stop != 0); if (__pyx_t_2) { - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -128274,7 +129611,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":855 + /* "View.MemoryView":859 * if have_stop: * if stop < 0: * stop += shape # <<<<<<<<<<<<<< @@ -128283,7 +129620,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -128293,7 +129630,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":857 + /* "View.MemoryView":861 * stop += shape * if stop < 0: * stop = 0 # <<<<<<<<<<<<<< @@ -128302,7 +129639,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = 0; - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -128311,7 +129648,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -128321,7 +129658,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L17; } - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -128331,7 +129668,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":859 + /* "View.MemoryView":863 * stop = 0 * elif stop > shape: * stop = shape # <<<<<<<<<<<<<< @@ -128340,7 +129677,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = __pyx_v_shape; - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -128350,7 +129687,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L17:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -128360,7 +129697,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L16; } - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -128371,7 +129708,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":862 + /* "View.MemoryView":866 * else: * if negative_step: * stop = -1 # <<<<<<<<<<<<<< @@ -128380,7 +129717,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = -1L; - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -128390,7 +129727,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L19; } - /* "View.MemoryView":864 + /* "View.MemoryView":868 * stop = -1 * else: * stop = shape # <<<<<<<<<<<<<< @@ -128404,7 +129741,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L16:; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -128414,7 +129751,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":867 + /* "View.MemoryView":871 * * if not have_step: * step = 1 # <<<<<<<<<<<<<< @@ -128423,7 +129760,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_step = 1; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -128432,7 +129769,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":871 + /* "View.MemoryView":875 * * with cython.cdivision(True): * new_shape = (stop - start) // step # <<<<<<<<<<<<<< @@ -128441,7 +129778,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -128451,7 +129788,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":874 + /* "View.MemoryView":878 * * if (stop - start) - step * new_shape: * new_shape += 1 # <<<<<<<<<<<<<< @@ -128460,7 +129797,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = (__pyx_v_new_shape + 1); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -128469,7 +129806,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -128479,7 +129816,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":877 + /* "View.MemoryView":881 * * if new_shape < 0: * new_shape = 0 # <<<<<<<<<<<<<< @@ -128488,7 +129825,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = 0; - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -128497,7 +129834,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":880 + /* "View.MemoryView":884 * * * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< @@ -128506,7 +129843,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - /* "View.MemoryView":881 + /* "View.MemoryView":885 * * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< @@ -128515,7 +129852,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - /* "View.MemoryView":882 + /* "View.MemoryView":886 * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< @@ -128526,7 +129863,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L3:; - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -128536,7 +129873,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":886 + /* "View.MemoryView":890 * * if suboffset_dim[0] < 0: * dst.data += start * stride # <<<<<<<<<<<<<< @@ -128545,7 +129882,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -128555,7 +129892,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L23; } - /* "View.MemoryView":888 + /* "View.MemoryView":892 * dst.data += start * stride * else: * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< @@ -128568,7 +129905,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L23:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -128578,7 +129915,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -128588,7 +129925,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -128598,7 +129935,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":893 + /* "View.MemoryView":897 * if not is_slice: * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< @@ -128607,7 +129944,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -128617,7 +129954,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L26; } - /* "View.MemoryView":895 + /* "View.MemoryView":899 * dst.data = ( dst.data)[0] + suboffset * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< @@ -128626,18 +129963,18 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ /*else*/ { - /* "View.MemoryView":896 + /* "View.MemoryView":900 * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< * else: * suboffset_dim[0] = new_ndim */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 895, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 899, __pyx_L1_error) } __pyx_L26:; - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -128647,7 +129984,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L25; } - /* "View.MemoryView":898 + /* "View.MemoryView":902 * "must be indexed and not sliced", dim) * else: * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< @@ -128659,7 +129996,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L25:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -128668,7 +130005,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":900 + /* "View.MemoryView":904 * suboffset_dim[0] = new_ndim * * return 0 # <<<<<<<<<<<<<< @@ -128678,7 +130015,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":803 + /* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -128702,7 +130039,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, return __pyx_r; } -/* "View.MemoryView":906 +/* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -128722,9 +130059,12 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("pybuffer_index", 0); - /* "View.MemoryView":908 + /* "View.MemoryView":912 * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< @@ -128733,7 +130073,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_suboffset = -1L; 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if (__pyx_t_2) { - /* "View.MemoryView":931 + /* "View.MemoryView":935 * resultp = bufp + index * stride * if suboffset >= 0: * resultp = ( resultp)[0] + suboffset # <<<<<<<<<<<<<< @@ -128970,7 +130310,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":930 + /* "View.MemoryView":934 * * resultp = bufp + index * stride * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -128979,7 +130319,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":933 + /* "View.MemoryView":937 * resultp = ( resultp)[0] + suboffset * * return resultp # <<<<<<<<<<<<<< @@ -128989,7 +130329,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_r = __pyx_v_resultp; goto __pyx_L0; - /* "View.MemoryView":906 + /* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -129008,7 +130348,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P return __pyx_r; 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(__pyx_v_strides[__pyx_v_j]) = __pyx_t_6; - /* "View.MemoryView":950 + /* "View.MemoryView":954 * j = ndim - 1 - i * strides[i], strides[j] = strides[j], strides[i] * shape[i], shape[j] = shape[j], shape[i] # <<<<<<<<<<<<<< @@ -129108,7 +130451,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { (__pyx_v_shape[__pyx_v_i]) = __pyx_t_6; (__pyx_v_shape[__pyx_v_j]) = __pyx_t_5; - /* "View.MemoryView":952 + /* "View.MemoryView":956 * shape[i], shape[j] = shape[j], shape[i] * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: # <<<<<<<<<<<<<< @@ -129126,16 +130469,16 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_L6_bool_binop_done:; if (__pyx_t_7) { - /* "View.MemoryView":953 + /* "View.MemoryView":957 * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: * _err(ValueError, "Cannot transpose memoryview with indirect dimensions") # <<<<<<<<<<<<<< * * return 1 */ - __pyx_t_9 = __pyx_memoryview_err(__pyx_builtin_ValueError, ((char *)"Cannot transpose memoryview with indirect dimensions")); 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if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 985, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_assign_item_from_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp, __pyx_v_value); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 989, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __pyx_L3:; - /* "View.MemoryView":981 + /* "View.MemoryView":985 * return memoryview.convert_item_to_object(self, itemp) * * cdef assign_item_from_object(self, char *itemp, object value): # <<<<<<<<<<<<<< @@ -129386,7 +130735,7 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo return __pyx_r; } -/* "View.MemoryView":988 +/* "View.MemoryView":992 * * @property * def base(self): # <<<<<<<<<<<<<< @@ -129412,7 +130761,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__", 0); - /* "View.MemoryView":989 + /* "View.MemoryView":993 * @property * def base(self): * return self.from_object # <<<<<<<<<<<<<< @@ -129424,7 +130773,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __pyx_r = __pyx_v_self->from_object; 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if (__pyx_t_1) { - /* "View.MemoryView":1024 + /* "View.MemoryView":1028 * * if (memviewslice.memview).flags & PyBUF_WRITABLE: * result.flags = PyBUF_RECORDS # <<<<<<<<<<<<<< @@ -129735,7 +131093,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.flags = PyBUF_RECORDS; - /* "View.MemoryView":1023 + /* "View.MemoryView":1027 * Py_INCREF(Py_None) * * if (memviewslice.memview).flags & PyBUF_WRITABLE: # <<<<<<<<<<<<<< @@ -129745,7 +131103,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl goto __pyx_L4; } - /* "View.MemoryView":1026 + /* "View.MemoryView":1030 * result.flags = PyBUF_RECORDS * else: * result.flags = PyBUF_RECORDS_RO # <<<<<<<<<<<<<< @@ -129757,7 +131115,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L4:; - /* "View.MemoryView":1028 + /* "View.MemoryView":1032 * result.flags = PyBUF_RECORDS_RO * * result.view.shape = result.from_slice.shape # <<<<<<<<<<<<<< @@ -129766,7 +131124,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.shape = ((Py_ssize_t *)__pyx_v_result->from_slice.shape); 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if (__pyx_t_1) { - /* "View.MemoryView":1035 + /* "View.MemoryView":1039 * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets # <<<<<<<<<<<<<< @@ -129815,7 +131173,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = ((Py_ssize_t *)__pyx_v_result->from_slice.suboffsets); - /* "View.MemoryView":1036 + /* "View.MemoryView":1040 * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets * break # <<<<<<<<<<<<<< @@ -129824,7 +131182,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ goto __pyx_L6_break; - /* "View.MemoryView":1034 + /* "View.MemoryView":1038 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -129835,7 +131193,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L6_break:; - /* "View.MemoryView":1038 + /* "View.MemoryView":1042 * break * * result.view.len = result.view.itemsize # <<<<<<<<<<<<<< @@ -129845,7 +131203,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_9 = __pyx_v_result->__pyx_base.view.itemsize; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; - /* "View.MemoryView":1039 + /* "View.MemoryView":1043 * * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: # <<<<<<<<<<<<<< @@ -129855,29 +131213,29 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_7 = (__pyx_v_result->__pyx_base.view.shape + __pyx_v_ndim); for (__pyx_t_8 = __pyx_v_result->__pyx_base.view.shape; __pyx_t_8 < __pyx_t_7; __pyx_t_8++) { __pyx_t_6 = __pyx_t_8; - __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1039, __pyx_L1_error) + __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1043, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF_SET(__pyx_v_length, __pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":1040 + /* "View.MemoryView":1044 * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: * result.view.len *= length # <<<<<<<<<<<<<< * * result.to_object_func = to_object_func */ - __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1040, __pyx_L1_error) + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1040, __pyx_L1_error) + __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(1, 1040, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(1, 1044, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; } - /* "View.MemoryView":1042 + /* "View.MemoryView":1046 * result.view.len *= length * * result.to_object_func = to_object_func # <<<<<<<<<<<<<< @@ -129886,7 +131244,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_object_func = __pyx_v_to_object_func; - /* "View.MemoryView":1043 + /* "View.MemoryView":1047 * * result.to_object_func = to_object_func * result.to_dtype_func = to_dtype_func # <<<<<<<<<<<<<< @@ -129895,7 +131253,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_dtype_func = __pyx_v_to_dtype_func; - /* "View.MemoryView":1045 + /* "View.MemoryView":1049 * result.to_dtype_func = to_dtype_func * * return result # <<<<<<<<<<<<<< @@ -129907,7 +131265,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":995 + /* "View.MemoryView":999 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -129929,11 +131287,11 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl return __pyx_r; } -/* "View.MemoryView":1048 +/* "View.MemoryView":1052 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *mslice): + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj */ @@ -129944,10 +131302,13 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p int __pyx_t_1; int __pyx_t_2; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_slice_from_memview", 0); - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -129957,20 +131318,20 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1052 + /* "View.MemoryView":1056 * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): * obj = memview # <<<<<<<<<<<<<< * return &obj.from_slice * else: */ - if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(1, 1052, __pyx_L1_error) + if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(1, 1056, __pyx_L1_error) __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_obj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":1053 + /* "View.MemoryView":1057 * if isinstance(memview, _memoryviewslice): * obj = memview * return &obj.from_slice # <<<<<<<<<<<<<< @@ -129980,8 +131341,8 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_r = (&__pyx_v_obj->from_slice); goto __pyx_L0; - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -129989,7 +131350,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p */ } - /* "View.MemoryView":1055 + /* "View.MemoryView":1059 * return &obj.from_slice * else: * slice_copy(memview, mslice) # <<<<<<<<<<<<<< @@ -129999,7 +131360,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, __pyx_v_mslice); - /* "View.MemoryView":1056 + /* "View.MemoryView":1060 * else: * slice_copy(memview, mslice) * return mslice # <<<<<<<<<<<<<< @@ -130010,26 +131371,26 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p goto __pyx_L0; } - /* "View.MemoryView":1048 + /* "View.MemoryView":1052 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *mslice): + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj */ /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_WriteUnraisable("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); - __pyx_r = 0; + __Pyx_AddTraceback("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_obj); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "View.MemoryView":1059 +/* "View.MemoryView":1063 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -130050,7 +131411,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem Py_ssize_t __pyx_t_5; __Pyx_RefNannySetupContext("slice_copy", 0); - /* "View.MemoryView":1063 + /* "View.MemoryView":1067 * cdef (Py_ssize_t*) shape, strides, suboffsets * * shape = memview.view.shape # <<<<<<<<<<<<<< @@ -130060,7 +131421,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.shape; __pyx_v_shape = __pyx_t_1; - /* "View.MemoryView":1064 + /* "View.MemoryView":1068 * * shape = memview.view.shape * strides = memview.view.strides # <<<<<<<<<<<<<< @@ -130070,7 +131431,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.strides; __pyx_v_strides = __pyx_t_1; - /* "View.MemoryView":1065 + /* "View.MemoryView":1069 * shape = memview.view.shape * strides = memview.view.strides * suboffsets = memview.view.suboffsets # <<<<<<<<<<<<<< @@ -130080,7 +131441,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.suboffsets; __pyx_v_suboffsets = __pyx_t_1; - /* "View.MemoryView":1067 + /* "View.MemoryView":1071 * suboffsets = memview.view.suboffsets * * dst.memview = <__pyx_memoryview *> memview # <<<<<<<<<<<<<< @@ -130089,7 +131450,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->memview = ((struct __pyx_memoryview_obj *)__pyx_v_memview); - /* "View.MemoryView":1068 + /* "View.MemoryView":1072 * * dst.memview = <__pyx_memoryview *> memview * dst.data = memview.view.buf # <<<<<<<<<<<<<< @@ -130098,7 +131459,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->data = ((char *)__pyx_v_memview->view.buf); - /* "View.MemoryView":1070 + /* "View.MemoryView":1074 * dst.data = memview.view.buf * * for dim in range(memview.view.ndim): # <<<<<<<<<<<<<< @@ -130110,7 +131471,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_dim = __pyx_t_4; - /* "View.MemoryView":1071 + /* "View.MemoryView":1075 * * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] # <<<<<<<<<<<<<< @@ -130119,7 +131480,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->shape[__pyx_v_dim]) = (__pyx_v_shape[__pyx_v_dim]); - /* "View.MemoryView":1072 + /* "View.MemoryView":1076 * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] # <<<<<<<<<<<<<< @@ -130128,7 +131489,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->strides[__pyx_v_dim]) = (__pyx_v_strides[__pyx_v_dim]); - /* "View.MemoryView":1073 + /* "View.MemoryView":1077 * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 # <<<<<<<<<<<<<< @@ -130143,7 +131504,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_5; } - /* "View.MemoryView":1059 + /* "View.MemoryView":1063 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -130155,7 +131516,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1076 +/* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -130168,9 +131529,12 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy", 0); - /* "View.MemoryView":1079 + /* "View.MemoryView":1083 * "Create a new memoryview object" * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -130179,7 +131543,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx */ __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_memviewslice)); - /* "View.MemoryView":1080 + /* "View.MemoryView":1084 * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) * return memoryview_copy_from_slice(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -130187,13 +131551,13 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx * @cname('__pyx_memoryview_copy_object_from_slice') */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 1080, __pyx_L1_error) + __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 1084, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "View.MemoryView":1076 + /* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -130212,7 +131576,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx return __pyx_r; } -/* "View.MemoryView":1083 +/* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -130230,9 +131594,12 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview PyObject *(*__pyx_t_3)(char *); int (*__pyx_t_4)(char *, PyObject *); PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy_from_slice", 0); - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -130243,7 +131610,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1091 + /* "View.MemoryView":1095 * * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func # <<<<<<<<<<<<<< @@ -130253,7 +131620,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; __pyx_v_to_object_func = __pyx_t_3; - /* "View.MemoryView":1092 + /* "View.MemoryView":1096 * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< @@ -130263,7 +131630,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; __pyx_v_to_dtype_func = __pyx_t_4; - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -130273,7 +131640,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview goto __pyx_L3; } - /* "View.MemoryView":1094 + /* "View.MemoryView":1098 * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func * else: * to_object_func = NULL # <<<<<<<<<<<<<< @@ -130283,7 +131650,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview /*else*/ { __pyx_v_to_object_func = NULL; - /* "View.MemoryView":1095 + /* "View.MemoryView":1099 * else: * to_object_func = NULL * to_dtype_func = NULL # <<<<<<<<<<<<<< @@ -130294,7 +131661,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview } __pyx_L3:; - /* "View.MemoryView":1097 + /* "View.MemoryView":1101 * to_dtype_func = NULL * * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< @@ -130303,20 +131670,20 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __Pyx_XDECREF(__pyx_r); - /* "View.MemoryView":1099 + /* "View.MemoryView":1103 * return memoryview_fromslice(memviewslice[0], memview.view.ndim, * to_object_func, to_dtype_func, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 1097, __pyx_L1_error) + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 1101, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":1083 + /* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -130335,7 +131702,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview return __pyx_r; } -/* "View.MemoryView":1105 +/* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -130347,7 +131714,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { Py_ssize_t __pyx_r; int __pyx_t_1; - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -130357,7 +131724,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_t_1 = ((__pyx_v_arg < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1107 + /* "View.MemoryView":1111 * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: * return -arg # <<<<<<<<<<<<<< @@ -130367,7 +131734,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_r = (-__pyx_v_arg); goto __pyx_L0; - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -130376,7 +131743,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { */ } - /* "View.MemoryView":1109 + /* "View.MemoryView":1113 * return -arg * else: * return arg # <<<<<<<<<<<<<< @@ -130388,7 +131755,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { goto __pyx_L0; } - /* "View.MemoryView":1105 + /* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -130401,7 +131768,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { return __pyx_r; } -/* "View.MemoryView":1112 +/* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -130419,7 +131786,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ int __pyx_t_3; int __pyx_t_4; - /* "View.MemoryView":1117 + /* "View.MemoryView":1121 * """ * cdef int i * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< @@ -130428,7 +131795,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = 0; - /* "View.MemoryView":1118 + /* "View.MemoryView":1122 * cdef int i * cdef Py_ssize_t c_stride = 0 * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< @@ -130437,7 +131804,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = 0; - /* "View.MemoryView":1120 + /* "View.MemoryView":1124 * cdef Py_ssize_t f_stride = 0 * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -130447,7 +131814,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -130457,7 +131824,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1122 + /* "View.MemoryView":1126 * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -130466,7 +131833,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1123 + /* "View.MemoryView":1127 * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -130475,7 +131842,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L4_break; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -130486,7 +131853,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L4_break:; - /* "View.MemoryView":1125 + /* "View.MemoryView":1129 * break * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -130498,7 +131865,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -130508,7 +131875,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1127 + /* "View.MemoryView":1131 * for i in range(ndim): * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -130517,7 +131884,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1128 + /* "View.MemoryView":1132 * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -130526,7 +131893,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L7_break; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -130537,7 +131904,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L7_break:; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -130547,7 +131914,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1131 + /* "View.MemoryView":1135 * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): * return 'C' # <<<<<<<<<<<<<< @@ -130557,7 +131924,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_r = 'C'; goto __pyx_L0; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -130566,7 +131933,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ } - /* "View.MemoryView":1133 + /* "View.MemoryView":1137 * return 'C' * else: * return 'F' # <<<<<<<<<<<<<< @@ -130578,7 +131945,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ goto __pyx_L0; } - /* "View.MemoryView":1112 + /* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -130591,7 +131958,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ return __pyx_r; } -/* "View.MemoryView":1136 +/* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -130612,7 +131979,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v Py_ssize_t __pyx_t_5; Py_ssize_t __pyx_t_6; - /* "View.MemoryView":1143 + /* "View.MemoryView":1147 * * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< @@ -130621,7 +131988,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_extent = (__pyx_v_src_shape[0]); - /* "View.MemoryView":1144 + /* "View.MemoryView":1148 * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< @@ -130630,7 +131997,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - /* "View.MemoryView":1145 + /* "View.MemoryView":1149 * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< @@ -130639,7 +132006,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_stride = (__pyx_v_src_strides[0]); - /* "View.MemoryView":1146 + /* "View.MemoryView":1150 * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< @@ -130648,7 +132015,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -130658,7 +132025,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -130678,7 +132045,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L5_bool_binop_done; } - /* "View.MemoryView":1150 + /* "View.MemoryView":1154 * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< @@ -130693,7 +132060,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = __pyx_t_3; __pyx_L5_bool_binop_done:; - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -130702,7 +132069,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ if (__pyx_t_1) { - /* "View.MemoryView":1151 + /* "View.MemoryView":1155 * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< @@ -130711,7 +132078,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -130721,7 +132088,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L4; } - /* "View.MemoryView":1153 + /* "View.MemoryView":1157 * memcpy(dst_data, src_data, itemsize * dst_extent) * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -130734,7 +132101,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1154 + /* "View.MemoryView":1158 * else: * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< @@ -130743,7 +132110,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - /* "View.MemoryView":1155 + /* "View.MemoryView":1159 * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -130752,7 +132119,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1156 + /* "View.MemoryView":1160 * memcpy(dst_data, src_data, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -130764,7 +132131,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L4:; - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -130774,7 +132141,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L3; } - /* "View.MemoryView":1158 + /* "View.MemoryView":1162 * dst_data += dst_stride * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -130787,7 +132154,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1159 + /* "View.MemoryView":1163 * else: * for i in range(dst_extent): * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< @@ -130796,7 +132163,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - /* "View.MemoryView":1163 + /* "View.MemoryView":1167 * src_shape + 1, dst_shape + 1, * ndim - 1, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -130805,7 +132172,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1164 + /* "View.MemoryView":1168 * ndim - 1, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -130817,7 +132184,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L3:; - /* "View.MemoryView":1136 + /* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -130828,7 +132195,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v /* function exit code */ } -/* "View.MemoryView":1166 +/* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -130838,7 +132205,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - /* "View.MemoryView":1169 + /* "View.MemoryView":1173 * __Pyx_memviewslice *dst, * int ndim, size_t itemsize) nogil: * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< @@ -130847,7 +132214,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi */ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1166 + /* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -130858,57 +132225,57 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi /* function exit code */ } -/* "View.MemoryView":1173 +/* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - int __pyx_v_i; + Py_ssize_t __pyx_v_shape; Py_ssize_t __pyx_v_size; Py_ssize_t __pyx_r; Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; + Py_ssize_t *__pyx_t_2; + Py_ssize_t *__pyx_t_3; + Py_ssize_t *__pyx_t_4; - /* "View.MemoryView":1176 + /* "View.MemoryView":1179 + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< * - * for i in range(ndim): + * for shape in src.shape[:ndim]: */ __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_size = __pyx_t_1; - /* "View.MemoryView":1178 - * cdef Py_ssize_t size = src.memview.view.itemsize + /* "View.MemoryView":1181 + * cdef Py_ssize_t shape, size = src.memview.view.itemsize * - * for i in range(ndim): # <<<<<<<<<<<<<< - * size *= src.shape[i] + * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< + * size *= shape * */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; + __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); + for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { + __pyx_t_2 = __pyx_t_4; + __pyx_v_shape = (__pyx_t_2[0]); - /* "View.MemoryView":1179 + /* "View.MemoryView":1182 * - * for i in range(ndim): - * size *= src.shape[i] # <<<<<<<<<<<<<< + * for shape in src.shape[:ndim]: + * size *= shape # <<<<<<<<<<<<<< * * return size */ - __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + __pyx_v_size = (__pyx_v_size * __pyx_v_shape); } - /* "View.MemoryView":1181 - * size *= src.shape[i] + /* "View.MemoryView":1184 + * size *= shape * * return size # <<<<<<<<<<<<<< * @@ -130917,12 +132284,12 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_r = __pyx_v_size; goto __pyx_L0; - /* "View.MemoryView":1173 + /* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ /* function exit code */ @@ -130930,7 +132297,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr return __pyx_r; } -/* "View.MemoryView":1184 +/* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -130946,7 +132313,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ int __pyx_t_3; int __pyx_t_4; - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -130956,38 +132323,38 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_t_1 = ((__pyx_v_order == 'F') != 0); if (__pyx_t_1) { - /* "View.MemoryView":1194 + /* "View.MemoryView":1197 * * if order == 'F': * for idx in range(ndim): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ __pyx_t_2 = __pyx_v_ndim; __pyx_t_3 = __pyx_t_2; for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_idx = __pyx_t_4; - /* "View.MemoryView":1195 + /* "View.MemoryView":1198 * if order == 'F': * for idx in range(ndim): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * else: */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1196 + /* "View.MemoryView":1199 * for idx in range(ndim): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * else: * for idx in range(ndim - 1, -1, -1): */ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); } - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -130997,30 +132364,30 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ goto __pyx_L3; } - /* "View.MemoryView":1198 - * stride = stride * shape[idx] + /* "View.MemoryView":1201 + * stride *= shape[idx] * else: * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ /*else*/ { for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; - /* "View.MemoryView":1199 + /* "View.MemoryView":1202 * else: * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1200 + /* "View.MemoryView":1203 * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * * return stride */ @@ -131029,8 +132396,8 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ } __pyx_L3:; - /* "View.MemoryView":1202 - * stride = stride * shape[idx] + /* "View.MemoryView":1205 + * stride *= shape[idx] * * return stride # <<<<<<<<<<<<<< * @@ -131039,7 +132406,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_r = __pyx_v_stride; goto __pyx_L0; - /* "View.MemoryView":1184 + /* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -131052,7 +132419,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ return __pyx_r; } -/* "View.MemoryView":1205 +/* "View.MemoryView":1208 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -131072,8 +132439,11 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, struct __pyx_memoryview_obj *__pyx_t_4; int __pyx_t_5; int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; - /* "View.MemoryView":1216 + /* "View.MemoryView":1219 * cdef void *result * * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -131083,7 +132453,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1217 + /* "View.MemoryView":1220 * * cdef size_t itemsize = src.memview.view.itemsize * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< @@ -131092,7 +132462,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - /* "View.MemoryView":1219 + /* "View.MemoryView":1222 * cdef size_t size = slice_get_size(src, ndim) * * result = malloc(size) # <<<<<<<<<<<<<< @@ -131101,7 +132471,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_result = malloc(__pyx_v_size); - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -131111,16 +132481,16 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1221 + /* "View.MemoryView":1224 * result = malloc(size) * if not result: * _err(MemoryError, NULL) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 1221, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 1224, __pyx_L1_error) - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -131129,7 +132499,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ } - /* "View.MemoryView":1224 + /* "View.MemoryView":1227 * * * tmpslice.data = result # <<<<<<<<<<<<<< @@ -131138,7 +132508,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - /* "View.MemoryView":1225 + /* "View.MemoryView":1228 * * tmpslice.data = result * tmpslice.memview = src.memview # <<<<<<<<<<<<<< @@ -131148,7 +132518,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_4 = __pyx_v_src->memview; __pyx_v_tmpslice->memview = __pyx_t_4; - /* "View.MemoryView":1226 + /* "View.MemoryView":1229 * tmpslice.data = result * tmpslice.memview = src.memview * for i in range(ndim): # <<<<<<<<<<<<<< @@ -131160,7 +132530,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1227 + /* "View.MemoryView":1230 * tmpslice.memview = src.memview * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< @@ -131169,7 +132539,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - /* "View.MemoryView":1228 + /* "View.MemoryView":1231 * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -131179,7 +132549,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1230 + /* "View.MemoryView":1233 * tmpslice.suboffsets[i] = -1 * * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< @@ -131188,7 +132558,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - /* "View.MemoryView":1234 + /* "View.MemoryView":1237 * * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -131200,7 +132570,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1235 + /* "View.MemoryView":1238 * * for i in range(ndim): * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< @@ -131210,7 +132580,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1236 + /* "View.MemoryView":1239 * for i in range(ndim): * if tmpslice.shape[i] == 1: * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< @@ -131219,7 +132589,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (__pyx_v_tmpslice->strides[__pyx_v_i]) = 0; - /* "View.MemoryView":1235 + /* "View.MemoryView":1238 * * for i in range(ndim): * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< @@ -131229,7 +132599,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, } } - /* "View.MemoryView":1238 + /* "View.MemoryView":1241 * tmpslice.strides[i] = 0 * * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< @@ -131239,7 +132609,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = (__pyx_memviewslice_is_contig((__pyx_v_src[0]), __pyx_v_order, __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1239 + /* "View.MemoryView":1242 * * if slice_is_contig(src[0], order, ndim): * memcpy(result, src.data, size) # <<<<<<<<<<<<<< @@ -131248,7 +132618,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size)); - /* "View.MemoryView":1238 + /* "View.MemoryView":1241 * tmpslice.strides[i] = 0 * * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< @@ -131258,7 +132628,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, goto __pyx_L9; } - /* "View.MemoryView":1241 + /* "View.MemoryView":1244 * memcpy(result, src.data, size) * else: * copy_strided_to_strided(src, tmpslice, ndim, itemsize) # <<<<<<<<<<<<<< @@ -131270,7 +132640,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, } __pyx_L9:; - /* "View.MemoryView":1243 + /* "View.MemoryView":1246 * copy_strided_to_strided(src, tmpslice, ndim, itemsize) * * return result # <<<<<<<<<<<<<< @@ -131280,7 +132650,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "View.MemoryView":1205 + /* "View.MemoryView":1208 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -131304,7 +132674,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, return __pyx_r; 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- /* "View.MemoryView":1286 + /* "View.MemoryView":1289 * broadcast_leading(&dst, dst_ndim, src_ndim) * * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -131724,7 +133106,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_v_ndim = __pyx_t_5; - /* "View.MemoryView":1288 + /* "View.MemoryView":1291 * cdef int ndim = max(src_ndim, dst_ndim) * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -131736,7 +133118,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -131746,7 +133128,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -131756,7 +133138,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1291 + /* "View.MemoryView":1294 * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: * broadcasting = True # <<<<<<<<<<<<<< @@ -131765,7 +133147,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 1; - /* "View.MemoryView":1292 + /* "View.MemoryView":1295 * if src.shape[i] == 1: * broadcasting = True * src.strides[i] = 0 # <<<<<<<<<<<<<< @@ -131774,7 +133156,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (__pyx_v_src.strides[__pyx_v_i]) = 0; - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -131784,7 +133166,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L7; } - /* "View.MemoryView":1294 + /* "View.MemoryView":1297 * src.strides[i] = 0 * else: * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< @@ -131792,11 +133174,11 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if src.suboffsets[i] >= 0: */ /*else*/ { - __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1294, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1297, __pyx_L1_error) } __pyx_L7:; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -131805,7 +133187,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -131815,16 +133197,16 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1297 + /* "View.MemoryView":1300 * * if src.suboffsets[i] >= 0: * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< * * if slices_overlap(&src, &dst, ndim, itemsize): */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1297, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1300, __pyx_L1_error) - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -131834,7 +133216,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } } - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -131844,7 +133226,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -131854,7 +133236,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1302 + /* "View.MemoryView":1305 * * if not slice_is_contig(src, order, ndim): * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< @@ -131863,7 +133245,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -131872,17 +133254,17 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1304 + /* "View.MemoryView":1307 * order = get_best_order(&dst, ndim) * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< * src = tmp * */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(1, 1304, __pyx_L1_error) + __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(1, 1307, __pyx_L1_error) __pyx_v_tmpdata = __pyx_t_7; - /* "View.MemoryView":1305 + /* "View.MemoryView":1308 * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) * src = tmp # <<<<<<<<<<<<<< @@ -131891,7 +133273,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_src = __pyx_v_tmp; - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -131900,7 +133282,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -131910,7 +133292,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -131920,7 +133302,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1311 + /* "View.MemoryView":1314 * * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< @@ -131929,7 +133311,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -131939,7 +133321,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L12; } - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -131949,7 +133331,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1313 + /* "View.MemoryView":1316 * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< @@ -131958,7 +133340,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -131968,7 +133350,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_L12:; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -131978,7 +133360,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_v_direct_copy != 0); if (__pyx_t_2) { - /* "View.MemoryView":1317 + /* "View.MemoryView":1320 * if direct_copy: * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -131987,7 +133369,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1318 + /* "View.MemoryView":1321 * * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< @@ -131996,7 +133378,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - /* "View.MemoryView":1319 + /* "View.MemoryView":1322 * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -132005,7 +133387,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1320 + /* "View.MemoryView":1323 * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) # <<<<<<<<<<<<<< @@ -132014,7 +133396,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1321 + /* "View.MemoryView":1324 * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -132024,7 +133406,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -132033,7 +133415,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -132042,7 +133424,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -132056,25 +133438,25 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_8 = (__pyx_t_2 != 0); if (__pyx_t_8) { - /* "View.MemoryView":1326 + /* "View.MemoryView":1329 * * * transpose_memslice(&src) # <<<<<<<<<<<<<< * transpose_memslice(&dst) * */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1326, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1329, __pyx_L1_error) - /* "View.MemoryView":1327 + /* "View.MemoryView":1330 * * transpose_memslice(&src) * transpose_memslice(&dst) # <<<<<<<<<<<<<< * * refcount_copying(&dst, dtype_is_object, ndim, False) */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1327, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1330, __pyx_L1_error) - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -132083,7 +133465,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1329 + /* "View.MemoryView":1332 * transpose_memslice(&dst) * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -132092,7 +133474,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1330 + /* "View.MemoryView":1333 * * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< @@ -132101,7 +133483,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1331 + /* "View.MemoryView":1334 * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -132110,7 +133492,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1333 + /* "View.MemoryView":1336 * refcount_copying(&dst, dtype_is_object, ndim, True) * * free(tmpdata) # <<<<<<<<<<<<<< @@ -132119,7 +133501,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1334 + /* "View.MemoryView":1337 * * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -132129,7 +133511,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1265 + /* "View.MemoryView":1268 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -132153,7 +133535,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ return __pyx_r; } -/* "View.MemoryView":1337 +/* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -132168,7 +133550,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1341 + /* "View.MemoryView":1344 * int ndim_other) nogil: * cdef int i * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< @@ -132177,7 +133559,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); - /* "View.MemoryView":1343 + /* "View.MemoryView":1346 * cdef int offset = ndim_other - ndim * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -132187,7 +133569,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1344 + /* "View.MemoryView":1347 * * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< @@ -132196,7 +133578,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); - /* "View.MemoryView":1345 + /* "View.MemoryView":1348 * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< @@ -132205,7 +133587,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1346 + /* "View.MemoryView":1349 * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< @@ -132215,7 +133597,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); } - /* "View.MemoryView":1348 + /* "View.MemoryView":1351 * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * * for i in range(offset): # <<<<<<<<<<<<<< @@ -132227,7 +133609,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1349 + /* "View.MemoryView":1352 * * for i in range(offset): * mslice.shape[i] = 1 # <<<<<<<<<<<<<< @@ -132236,7 +133618,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[__pyx_v_i]) = 1; - /* "View.MemoryView":1350 + /* "View.MemoryView":1353 * for i in range(offset): * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< @@ -132245,7 +133627,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); - /* "View.MemoryView":1351 + /* "View.MemoryView":1354 * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] * mslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -132255,7 +133637,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1337 + /* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -132266,7 +133648,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic /* function exit code */ } -/* "View.MemoryView":1359 +/* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -132277,7 +133659,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { int __pyx_t_1; - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -132287,7 +133669,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __pyx_t_1 = (__pyx_v_dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":1364 + /* "View.MemoryView":1367 * * if dtype_is_object: * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< @@ -132296,7 +133678,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -132305,7 +133687,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ } - /* "View.MemoryView":1359 + /* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -132316,7 +133698,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i /* function exit code */ } -/* "View.MemoryView":1368 +/* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132331,7 +133713,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0); - /* "View.MemoryView":1371 + /* "View.MemoryView":1374 * Py_ssize_t *strides, int ndim, * bint inc) with gil: * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<< @@ -132340,7 +133722,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1368 + /* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132355,7 +133737,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif } -/* "View.MemoryView":1374 +/* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132372,7 +133754,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss int __pyx_t_4; __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); - /* "View.MemoryView":1378 + /* "View.MemoryView":1381 * cdef Py_ssize_t i * * for i in range(shape[0]): # <<<<<<<<<<<<<< @@ -132384,7 +133766,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -132394,7 +133776,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_4) { - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -132404,7 +133786,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = (__pyx_v_inc != 0); if (__pyx_t_4) { - /* "View.MemoryView":1381 + /* "View.MemoryView":1384 * if ndim == 1: * if inc: * Py_INCREF(( data)[0]) # <<<<<<<<<<<<<< @@ -132413,7 +133795,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ Py_INCREF((((PyObject **)__pyx_v_data)[0])); - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -132423,7 +133805,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L6; } - /* "View.MemoryView":1383 + /* "View.MemoryView":1386 * Py_INCREF(( data)[0]) * else: * Py_DECREF(( data)[0]) # <<<<<<<<<<<<<< @@ -132435,7 +133817,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L6:; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -132445,7 +133827,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L5; } - /* "View.MemoryView":1385 + /* "View.MemoryView":1388 * Py_DECREF(( data)[0]) * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -132454,7 +133836,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ /*else*/ { - /* "View.MemoryView":1386 + /* "View.MemoryView":1389 * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, * ndim - 1, inc) # <<<<<<<<<<<<<< @@ -132465,7 +133847,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L5:; - /* "View.MemoryView":1388 + /* "View.MemoryView":1391 * ndim - 1, inc) * * data += strides[0] # <<<<<<<<<<<<<< @@ -132475,7 +133857,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_v_data = (__pyx_v_data + (__pyx_v_strides[0])); } - /* "View.MemoryView":1374 + /* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132487,7 +133869,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1394 +/* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -132497,7 +133879,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item, int __pyx_v_dtype_is_object) { - /* "View.MemoryView":1397 + /* "View.MemoryView":1400 * size_t itemsize, void *item, * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -132506,7 +133888,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1398 + /* "View.MemoryView":1401 * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< @@ -132515,7 +133897,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1400 + /* "View.MemoryView":1403 * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, * itemsize, item) * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -132524,7 +133906,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1394 + /* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -132535,7 +133917,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst /* function exit code */ } -/* "View.MemoryView":1404 +/* "View.MemoryView":1407 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132552,7 +133934,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t Py_ssize_t __pyx_t_3; Py_ssize_t __pyx_t_4; - /* "View.MemoryView":1408 + /* "View.MemoryView":1411 * size_t itemsize, void *item) nogil: * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] # <<<<<<<<<<<<<< @@ -132561,7 +133943,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_stride = (__pyx_v_strides[0]); - /* "View.MemoryView":1409 + /* "View.MemoryView":1412 * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] * cdef Py_ssize_t extent = shape[0] # <<<<<<<<<<<<<< @@ -132570,7 +133952,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_extent = (__pyx_v_shape[0]); - /* "View.MemoryView":1411 + /* "View.MemoryView":1414 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -132580,7 +133962,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1412 + /* "View.MemoryView":1415 * * if ndim == 1: * for i in range(extent): # <<<<<<<<<<<<<< @@ -132592,7 +133974,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1413 + /* "View.MemoryView":1416 * if ndim == 1: * for i in range(extent): * memcpy(data, item, itemsize) # <<<<<<<<<<<<<< @@ -132601,7 +133983,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize)); - /* "View.MemoryView":1414 + /* "View.MemoryView":1417 * for i in range(extent): * memcpy(data, item, itemsize) * data += stride # <<<<<<<<<<<<<< @@ -132611,7 +133993,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_v_data = (__pyx_v_data + __pyx_v_stride); } - /* "View.MemoryView":1411 + /* "View.MemoryView":1414 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -132621,7 +134003,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t goto __pyx_L3; } - /* "View.MemoryView":1416 + /* "View.MemoryView":1419 * data += stride * else: * for i in range(extent): # <<<<<<<<<<<<<< @@ -132634,7 +134016,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1417 + /* "View.MemoryView":1420 * else: * for i in range(extent): * _slice_assign_scalar(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -132643,7 +134025,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_memoryview__slice_assign_scalar(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1419 + /* "View.MemoryView":1422 * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) * data += stride # <<<<<<<<<<<<<< @@ -132655,7 +134037,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t } __pyx_L3:; - /* "View.MemoryView":1404 + /* "View.MemoryView":1407 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -132679,6 +134061,9 @@ static PyObject *__pyx_pw_15View_dot_MemoryView_1__pyx_unpickle_Enum(PyObject *_ PyObject *__pyx_v___pyx_type = 0; long __pyx_v___pyx_checksum; PyObject *__pyx_v___pyx_state = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_unpickle_Enum (wrapper)", 0); @@ -132756,6 +134141,9 @@ static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSE PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_unpickle_Enum", 0); /* "(tree fragment)":4 @@ -132944,6 +134332,9 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ PyObject *__pyx_t_6 = NULL; PyObject *__pyx_t_7 = NULL; PyObject *__pyx_t_8 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_unpickle_Enum__set_state", 0); /* "(tree fragment)":12 @@ -133090,7 +134481,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_InputStreamBase = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_InputStreamBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133143,6 +134539,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_InputStreamBase = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_FileInputStream __pyx_vtable_5allel_3opt_11io_vcf_read_FileInputStream; @@ -133168,9 +134567,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_FileInputStream(PyObject { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_15FileInputStream_3__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->fileobj); @@ -133215,7 +134614,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_FileInputStream = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_FileInputStream), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_FileInputStream, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133268,6 +134672,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_FileInputStream = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_CharVectorInputStream __pyx_vtable_5allel_3opt_11io_vcf_read_CharVectorInputStream; @@ -133293,9 +134700,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_CharVectorInputStream(PyO { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_21CharVectorInputStream_3__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_InputStreamBase(o); @@ -133313,7 +134720,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_CharVectorInputStream = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_CharVectorInputStream), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_CharVectorInputStream, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133366,6 +134778,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_CharVectorInputStream = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static PyObject *__pyx_tp_new_5allel_3opt_11io_vcf_read_VCFContext(PyTypeObject *t, PyObject *a, PyObject *k) { @@ -133399,9 +134814,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFContext(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_10VCFContext_3__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->headers); @@ -133452,7 +134867,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFContext = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFContext, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133505,6 +134925,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFContext = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static PyObject *__pyx_tp_new_5allel_3opt_11io_vcf_read_VCFChunkIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { @@ -133582,7 +135005,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFChunkIterator = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFChunkIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFChunkIterator, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133635,6 +135063,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFChunkIterator = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFParser; @@ -133773,7 +135204,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133826,6 +135262,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase __pyx_vtable_5allel_3opt_11io_vcf_read_VCFFieldParserBase; @@ -133904,7 +135343,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFieldParserBase = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFieldParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -133957,6 +135401,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFieldParserBase = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFSkipFieldParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFSkipFieldParser; @@ -133981,7 +135428,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFSkipFieldParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFSkipFieldParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFieldParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134034,6 +135486,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFSkipFieldParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFChromPosParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFChromPosParser; @@ -134106,7 +135561,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFChromPosParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFChromPosParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFChromPosParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134159,6 +135619,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFChromPosParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFIDStringParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFIDStringParser; @@ -134198,7 +135661,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFIDStringParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFIDStringParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFIDStringParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134251,6 +135719,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFIDStringParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFIDObjectParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFIDObjectParser; @@ -134275,7 +135746,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFIDObjectParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFIDObjectParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFieldParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134328,6 +135804,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFIDObjectParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFRefStringParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFRefStringParser; @@ -134367,7 +135846,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFRefStringParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFRefStringParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFRefStringParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134420,6 +135904,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFRefStringParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFRefObjectParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFRefObjectParser; @@ -134444,7 +135931,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFRefObjectParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFRefObjectParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFieldParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134497,6 +135989,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFRefObjectParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFAltStringParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFAltStringParser; @@ -134583,7 +136078,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFAltStringParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltStringParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFAltStringParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134636,6 +136136,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFAltStringParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFAltObjectParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFAltObjectParser; @@ -134719,7 +136222,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFAltObjectParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltObjectParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFAltObjectParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134772,6 +136280,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFAltObjectParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFQualParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFQualParser; @@ -134811,7 +136322,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFQualParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFQualParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFQualParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134864,6 +136380,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFQualParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFilterParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFFilterParser; @@ -134894,9 +136413,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFilterParser(PyObject { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_15VCFFilterParser_5__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->filter_keys); @@ -134937,7 +136456,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFilterParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFilterParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFilterParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -134990,6 +136514,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFilterParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoParser; @@ -135021,9 +136548,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoParser(PyObject *o { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_13VCFInfoParser_5__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->info_keys); @@ -135084,7 +136611,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135137,6 +136669,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParserBase __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoParserBase; @@ -135215,7 +136750,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoParserBase = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoParserBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135268,6 +136808,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoParserBase = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser; @@ -135307,7 +136850,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135360,6 +136908,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt8Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser; @@ -135399,7 +136950,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135452,6 +137008,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt16Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser; @@ -135491,7 +137050,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135544,6 +137108,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt32Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser; @@ -135583,7 +137150,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135636,6 +137208,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoInt64Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser; @@ -135675,7 +137250,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135728,6 +137308,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt8Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser; @@ -135767,7 +137350,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135820,6 +137408,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt16Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser; @@ -135859,7 +137450,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -135912,6 +137508,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt32Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser; @@ -135951,7 +137550,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136004,6 +137608,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoUInt64Parser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser; @@ -136043,7 +137650,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136096,6 +137708,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFloat32Parser = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser; @@ -136135,7 +137750,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136188,6 +137808,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFloat64Parser = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoFlagParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoFlagParser; @@ -136227,7 +137850,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFlagParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoFlagParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoFlagParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136280,6 +137908,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoFlagParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoStringParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoStringParser; @@ -136319,7 +137950,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoStringParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoStringParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoStringParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136372,6 +138008,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoStringParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoObjectParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoObjectParser; @@ -136396,7 +138035,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoObjectParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoObjectParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136449,6 +138093,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoObjectParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoSkipParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFInfoSkipParser; @@ -136473,7 +138120,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoSkipParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoSkipParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFInfoParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136526,6 +138178,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFInfoSkipParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFormatParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFFormatParser; @@ -136554,9 +138209,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFormatParser(PyObject { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_15VCFFormatParser_5__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->format_keys); @@ -136596,7 +138251,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFormatParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFormatParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFormatParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136649,6 +138309,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFFormatParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParser; @@ -136673,7 +138336,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFFieldParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136730,6 +138398,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataParser; @@ -136762,9 +138433,9 @@ static void __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataParser(PyObjec { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_5allel_3opt_11io_vcf_read_17VCFCallDataParser_5__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->format_keys); @@ -136819,7 +138490,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataParser = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -136872,6 +138548,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataParser = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataParserBase __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataParserBase; @@ -136950,7 +138629,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataParserBase = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataParserBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137003,6 +138687,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataParserBase = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataSkipParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataSkipParser; @@ -137027,7 +138714,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataSkipParser = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataSkipParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataParserBase, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137080,6 +138772,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataSkipParser = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser; @@ -137119,7 +138814,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137172,6 +138872,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt8Parser = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser; @@ -137211,7 +138914,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137264,6 +138972,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt16Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser; @@ -137303,7 +139014,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137356,6 +139072,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt32Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser; @@ -137395,7 +139114,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137448,6 +139172,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeInt64Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser; @@ -137487,7 +139214,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137540,6 +139272,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt8Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser; @@ -137579,7 +139314,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137632,6 +139372,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt16Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser; @@ -137671,7 +139414,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137724,6 +139472,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt32Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser; @@ -137763,7 +139514,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137816,6 +139572,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeUInt64Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser; @@ -137855,7 +139614,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -137908,6 +139672,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt8Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parser; @@ -137947,7 +139714,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138000,6 +139772,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt16Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parser; @@ -138039,7 +139814,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138092,6 +139872,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt32Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parser; @@ -138131,7 +139914,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138184,6 +139972,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACInt64Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parser; @@ -138223,7 +140014,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138276,6 +140072,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt8Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Parser; @@ -138315,7 +140114,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Pars sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138368,6 +140172,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt16Pars #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Parser; @@ -138407,7 +140214,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Pars sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138460,6 +140272,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt32Pars #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Parser; @@ -138499,7 +140314,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Pars sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138552,6 +140372,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFGenotypeACUInt64Pars #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser; @@ -138591,7 +140414,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser = sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138644,6 +140472,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt8Parser = #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser; @@ -138683,7 +140514,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138736,6 +140572,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt16Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser; @@ -138775,7 +140614,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138828,6 +140672,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt32Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser; @@ -138867,7 +140714,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -138920,6 +140772,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataInt64Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser; @@ -138959,7 +140814,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139012,6 +140872,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt8Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser; @@ -139051,7 +140914,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139104,6 +140972,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt16Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser; @@ -139143,7 +141014,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139196,6 +141072,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt32Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser; @@ -139235,7 +141114,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139288,6 +141172,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataUInt64Parser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parser; @@ -139327,7 +141214,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139380,6 +141272,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataFloat32Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parser; @@ -139419,7 +141314,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parse sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139472,6 +141372,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataFloat64Parse #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataStringParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataStringParser; @@ -139511,7 +141414,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataStringParser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataStringParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataStringParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139564,6 +141472,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataStringParser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser __pyx_vtable_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser; @@ -139603,7 +141514,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139656,6 +141572,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_VCFCallDataObjectParser #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static PyObject *__pyx_tp_new_5allel_3opt_11io_vcf_read_ANNTransformer(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { @@ -139726,7 +141645,12 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_ANNTransformer = { sizeof(struct __pyx_obj_5allel_3opt_11io_vcf_read_ANNTransformer), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5allel_3opt_11io_vcf_read_ANNTransformer, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139779,6 +141703,9 @@ static PyTypeObject __pyx_type_5allel_3opt_11io_vcf_read_ANNTransformer = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_array __pyx_vtable_array; @@ -139812,9 +141739,9 @@ static void __pyx_tp_dealloc_array(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_array___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->mode); @@ -139907,7 +141834,12 @@ static PyTypeObject __pyx_type___pyx_array = { sizeof(struct __pyx_array_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_array, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -139960,6 +141892,9 @@ static PyTypeObject __pyx_type___pyx_array = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { @@ -140018,7 +141953,12 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_Enum, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -140071,6 +142011,9 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; @@ -140107,9 +142050,9 @@ static void __pyx_tp_dealloc_memoryview(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_memoryview___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->obj); @@ -140271,7 +142214,12 @@ static PyTypeObject __pyx_type___pyx_memoryview = { sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -140324,6 +142272,9 @@ static PyTypeObject __pyx_type___pyx_memoryview = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; 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- __Pyx_GIVEREF(__pyx_tuple__44); + __pyx_tuple__42 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__42)) __PYX_ERR(1, 136, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__42); + __Pyx_GIVEREF(__pyx_tuple__42); /* "View.MemoryView":148 * @@ -141403,9 +143338,9 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__45 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__45)) __PYX_ERR(1, 148, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__45); - __Pyx_GIVEREF(__pyx_tuple__45); + __pyx_tuple__43 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__43)) __PYX_ERR(1, 148, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__43); + __Pyx_GIVEREF(__pyx_tuple__43); /* "View.MemoryView":176 * self.data = malloc(self.len) @@ -141414,9 +143349,9 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { * * if self.dtype_is_object: */ - __pyx_tuple__46 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); 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__pyx_t_20 = 0; PyType_Modified(__pyx_memoryview_type); - /* "View.MemoryView":991 + /* "View.MemoryView":995 * return self.from_object * * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< * * */ - __pyx_t_20 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), ((char *)"getbuffer(obj, view, flags)")); if (unlikely(!__pyx_t_20)) __PYX_ERR(1, 991, __pyx_L1_error) + __pyx_t_20 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), ((char *)"getbuffer(obj, view, flags)")); if (unlikely(!__pyx_t_20)) __PYX_ERR(1, 995, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_20); - if (PyDict_SetItem((PyObject *)__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_20) < 0) __PYX_ERR(1, 991, __pyx_L1_error) + if (PyDict_SetItem((PyObject *)__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_20) < 0) __PYX_ERR(1, 995, __pyx_L1_error) __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; PyType_Modified(__pyx_memoryviewslice_type); @@ -145837,7 +147783,7 @@ static int __Pyx_ParseOptionalKeywords( } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + if (likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { @@ -145864,7 +147810,7 @@ static int __Pyx_ParseOptionalKeywords( while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -145880,7 +147826,7 @@ static int __Pyx_ParseOptionalKeywords( while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -145997,7 +147943,7 @@ static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args return result; } #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); PyObject *globals = PyFunction_GET_GLOBALS(func); PyObject *argdefs = PyFunction_GET_DEFAULTS(func); @@ -146068,12 +148014,12 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, } #if PY_MAJOR_VERSION >= 3 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, kwdefs, closure); #else result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, closure); #endif @@ -146725,7 +148671,7 @@ __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, int i, retval=-1; Py_buffer *buf = &memview->view; __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (memviewslice->memview || memviewslice->data) { + if (unlikely(memviewslice->memview || memviewslice->data)) { PyErr_SetString(PyExc_ValueError, "memviewslice is already initialized!"); goto fail; @@ -146804,13 +148750,13 @@ __Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int first_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview || (PyObject *) memview == Py_None) + if (unlikely(!memview || (PyObject *) memview == Py_None)) return; - if (__pyx_get_slice_count(memview) < 0) + if (unlikely(__pyx_get_slice_count(memview) < 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); first_time = __pyx_add_acquisition_count(memview) == 0; - if (first_time) { + if (unlikely(first_time)) { if (have_gil) { Py_INCREF((PyObject *) memview); } else { @@ -146824,18 +148770,16 @@ static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int last_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview ) { - return; - } else if ((PyObject *) memview == Py_None) { + if (unlikely(!memview || (PyObject *) memview == Py_None)) { memslice->memview = NULL; return; } - if (__pyx_get_slice_count(memview) <= 0) + if (unlikely(__pyx_get_slice_count(memview) <= 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); last_time = __pyx_sub_acquisition_count(memview) == 1; memslice->data = NULL; - if (last_time) { + if (unlikely(last_time)) { if (have_gil) { Py_CLEAR(memslice->memview); } else { @@ -148241,7 +150185,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { { #if PY_MAJOR_VERSION >= 3 if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { + if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); if (!module) { @@ -148468,9 +150412,9 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) if (stop < 0) stop += length; } - length = stop - start; - if (unlikely(length <= 0)) + if (unlikely(stop <= start)) return PyUnicode_FromUnicode(NULL, 0); + length = stop - start; cstring += start; if (decode_func) { return decode_func(cstring, length, errors); @@ -148718,6 +150662,28 @@ static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_nam return -1; } +/* PyObjectGetAttrStrNoError */ + static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + __Pyx_PyErr_Clear(); +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { + return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); + } +#endif + result = __Pyx_PyObject_GetAttrStr(obj, attr_name); + if (unlikely(!result)) { + __Pyx_PyObject_GetAttrStr_ClearAttributeError(); + } + return result; +} + /* SetupReduce */ static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { int ret; @@ -148745,43 +150711,51 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { PyObject *setstate = NULL; PyObject *setstate_cython = NULL; #if CYTHON_USE_PYTYPE_LOOKUP - if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #else - if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #endif #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; if (reduce_ex == object_reduce_ex) { #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); + if (likely(reduce_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (reduce == object_reduce || PyErr_Occurred()) { + goto __PYX_BAD; + } setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); if (!setstate) PyErr_Clear(); if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); + if (likely(setstate_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (!setstate || PyErr_Occurred()) { + goto __PYX_BAD; + } } PyType_Modified((PyTypeObject*)type_obj); } } - goto GOOD; -BAD: + goto __PYX_GOOD; +__PYX_BAD: if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); ret = -1; -GOOD: +__PYX_GOOD: #if !CYTHON_USE_PYTYPE_LOOKUP Py_XDECREF(object_reduce); Py_XDECREF(object_reduce_ex); @@ -148857,7 +150831,7 @@ static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, /* CLineInTraceback */ #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { +static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int c_line) { PyObject *use_cline; PyObject *ptype, *pvalue, *ptraceback; #if CYTHON_COMPILING_IN_CPYTHON @@ -148961,7 +150935,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } @@ -149065,7 +151039,6 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); @@ -149079,7 +151052,6 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return; } if ((0)) {} - else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); view->obj = NULL; Py_DECREF(obj); } @@ -149320,6 +151292,7 @@ static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { + case '?': return "'bool'"; case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; @@ -149362,7 +151335,7 @@ static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { - case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); @@ -149446,7 +151419,7 @@ static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; - case 'B': case 'H': case 'I': case 'L': case 'Q': + case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); @@ -149590,9 +151563,7 @@ static PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->ndim; -; + int i = 0, number, ndim; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, @@ -149600,6 +151571,7 @@ __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ndim = ctx->head->field->type->ndim; while (*ts && *ts != ')') { switch (*ts) { case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; @@ -149725,12 +151697,12 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha return NULL; } CYTHON_FALLTHROUGH; - case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 'p': - if (ctx->enc_type == *ts && got_Z == ctx->is_complex && - ctx->enc_packmode == ctx->new_packmode) { + if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && + (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { ctx->enc_count += ctx->new_count; ctx->new_count = 1; got_Z = 0; @@ -149816,13 +151788,13 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) if (buf->strides) { if (spec & __Pyx_MEMVIEW_CONTIG) { if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (buf->strides[dim] != sizeof(void *)) { + if (unlikely(buf->strides[dim] != sizeof(void *))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly contiguous " "in dimension %d.", dim); goto fail; } - } else if (buf->strides[dim] != buf->itemsize) { + } else if (unlikely(buf->strides[dim] != buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -149833,7 +151805,7 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) Py_ssize_t stride = buf->strides[dim]; if (stride < 0) stride = -stride; - if (stride < buf->itemsize) { + if (unlikely(stride < buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -149841,17 +151813,17 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) } } } else { - if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not contiguous in " "dimension %d", dim); goto fail; - } else if (spec & (__Pyx_MEMVIEW_PTR)) { + } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not indirect in " "dimension %d", dim); goto fail; - } else if (buf->suboffsets) { + } else if (unlikely(buf->suboffsets)) { PyErr_SetString(PyExc_ValueError, "Buffer exposes suboffsets but no strides"); goto fail; @@ -149865,7 +151837,7 @@ static int __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) { if (spec & __Pyx_MEMVIEW_DIRECT) { - if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { PyErr_Format(PyExc_ValueError, "Buffer not compatible with direct access " "in dimension %d.", dim); @@ -149873,7 +151845,7 @@ __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec } } if (spec & __Pyx_MEMVIEW_PTR) { - if (!buf->suboffsets || (buf->suboffsets[dim] < 0)) { + if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly accessible " "in dimension %d.", dim); @@ -149891,9 +151863,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) if (c_or_f_flag & __Pyx_IS_F_CONTIG) { Py_ssize_t stride = 1; for (i = 0; i < ndim; i++) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) - { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not fortran contiguous."); goto fail; @@ -149903,8 +151873,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { Py_ssize_t stride = 1; for (i = ndim - 1; i >- 1; i--) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not C contiguous."); goto fail; @@ -149945,7 +151914,7 @@ static int __Pyx_ValidateAndInit_memviewslice( goto fail; } buf = &memview->view; - if (buf->ndim != ndim) { + if (unlikely(buf->ndim != ndim)) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", ndim, buf->ndim); @@ -149953,9 +151922,9 @@ static int __Pyx_ValidateAndInit_memviewslice( } if (new_memview) { __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; } - if ((unsigned) buf->itemsize != dtype->size) { + if (unlikely((unsigned) buf->itemsize != dtype->size)) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", @@ -149968,12 +151937,12 @@ static int __Pyx_ValidateAndInit_memviewslice( } for (i = 0; i < ndim; i++) { spec = axes_specs[i]; - if (!__pyx_check_strides(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) goto fail; - if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) goto fail; } - if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) goto fail; if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, new_memview != NULL) == -1)) { @@ -151053,7 +153022,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_float64_t(const cha case 1: return a; case 2: - z = __Pyx_c_prod_float(a, a); return __Pyx_c_prod_float(a, a); case 3: z = __Pyx_c_prod_float(a, a); @@ -151208,7 +153176,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_float64_t(const cha case 1: return a; case 2: - z = __Pyx_c_prod_double(a, a); return __Pyx_c_prod_double(a, a); case 3: z = __Pyx_c_prod_double(a, a); @@ -151295,7 +153262,7 @@ __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, struct __pyx_memoryview_obj *memview_obj = NULL; __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); for (i = 0; i < ndim; i++) { - if (from_mvs->suboffsets[i] >= 0) { + if (unlikely(from_mvs->suboffsets[i] >= 0)) { PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " "indirect dimensions (axis %d)", i); goto fail; diff --git a/allel/opt/model.c b/allel/opt/model.c index 01b8bd7a..52fb150e 100644 --- a/allel/opt/model.c +++ b/allel/opt/model.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.29.10 */ +/* Generated by Cython 0.29.20 */ /* BEGIN: Cython Metadata { @@ -20,8 +20,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_10" -#define CYTHON_HEX_VERSION 0x001D0AF0 +#define CYTHON_ABI "0_29_20" +#define CYTHON_HEX_VERSION 0x001D14F0 #define CYTHON_FUTURE_DIVISION 1 #include #ifndef offsetof @@ -323,12 +323,12 @@ END: Cython Metadata */ #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" -#if PY_VERSION_HEX < 0x030800A4 +#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2 #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #define __Pyx_DefaultClassType PyType_Type #endif @@ -497,8 +497,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact +#ifndef PyObject_Unicode #define PyObject_Unicode PyObject_Str #endif +#endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) @@ -509,6 +511,13 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif +#if PY_VERSION_HEX >= 0x030900A4 + #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) +#else + #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) +#endif #if CYTHON_ASSUME_SAFE_MACROS #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) #else @@ -589,11 +598,10 @@ static CYTHON_INLINE float __PYX_NAN() { #define __Pyx_truncl truncl #endif - +#define __PYX_MARK_ERR_POS(f_index, lineno) \ + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } #define __PYX_ERR(f_index, lineno, Ln_error) \ -{ \ - __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ -} + { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } #ifndef __PYX_EXTERN_C #ifdef __cplusplus @@ -610,6 +618,9 @@ static CYTHON_INLINE float __PYX_NAN() { #include #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" + + /* NumPy API declarations from "numpy/__init__.pxd" */ + #include "pythread.h" #include #include "pystate.h" @@ -957,7 +968,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":697 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -966,7 +977,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":698 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -975,7 +986,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":699 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -984,7 +995,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":700 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -993,7 +1004,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":704 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1002,7 +1013,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":705 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1011,7 +1022,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":706 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1020,7 +1031,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":707 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1029,7 +1040,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":711 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1038,7 +1049,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":712 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1047,7 +1058,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":721 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1056,7 +1067,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":722 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1065,7 +1076,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":723 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1074,7 +1085,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":725 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1083,7 +1094,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":726 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1092,7 +1103,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":727 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1101,7 +1112,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":729 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1110,7 +1121,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":730 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1119,7 +1130,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":732 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1128,7 +1139,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":733 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1137,7 +1148,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":734 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1176,7 +1187,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":736 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1185,7 +1196,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":737 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1194,7 +1205,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":738 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1203,7 +1214,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":740 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1353,7 +1364,7 @@ struct __pyx_memoryview_obj { }; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -1404,7 +1415,7 @@ struct __pyx_vtabstruct_memoryview { static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -1532,7 +1543,7 @@ static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObje #define __Pyx_PyFunction_FastCall(func, args, nargs)\ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); #else #define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) #endif @@ -1708,7 +1719,7 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -1930,7 +1941,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -1958,11 +1969,6 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); /* None.proto */ static CYTHON_INLINE long __Pyx_div_long(long, long); -/* WriteUnraisableException.proto */ -static void __Pyx_WriteUnraisable(const char *name, int clineno, - int lineno, const char *filename, - int full_traceback, int nogil); - /* ImportFrom.proto */ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); @@ -1986,6 +1992,9 @@ static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_nam /* SetVTable.proto */ static int __Pyx_SetVtable(PyObject *dict, void *vtable); +/* PyObjectGetAttrStrNoError.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); + /* SetupReduce.proto */ static int __Pyx_setup_reduce(PyObject* type_obj); @@ -2003,7 +2012,7 @@ static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, /* FetchCommonType.proto */ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); -/* CythonFunction.proto */ +/* CythonFunctionShared.proto */ #define __Pyx_CyFunction_USED 1 #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 @@ -2031,6 +2040,7 @@ typedef struct { PyObject *func_classobj; void *defaults; int defaults_pyobjects; + size_t defaults_size; // used by FusedFunction for copying defaults int flags; PyObject *defaults_tuple; PyObject *defaults_kwdict; @@ -2039,9 +2049,7 @@ typedef struct { } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; #define __Pyx_CyFunction_Check(obj) (__Pyx_TypeCheck(obj, __pyx_CyFunctionType)) -#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ - __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) -static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *self, PyObject *module, PyObject *globals, @@ -2064,11 +2072,8 @@ typedef struct { PyObject *type; PyObject *self; } __pyx_FusedFunctionObject; -#define __pyx_FusedFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ - __pyx_FusedFunction_New(__pyx_FusedFunctionType, ml, flags, qualname, self, module, globals, code) -static PyObject *__pyx_FusedFunction_New(PyTypeObject *type, - PyMethodDef *ml, int flags, - PyObject *qualname, PyObject *self, +static PyObject *__pyx_FusedFunction_New(PyMethodDef *ml, int flags, + PyObject *qualname, PyObject *closure, PyObject *module, PyObject *globals, PyObject *code); static int __pyx_FusedFunction_clear(__pyx_FusedFunctionObject *self); @@ -2627,8 +2632,8 @@ int __pyx_module_is_main_allel__opt__model = 0; /* Implementation of 'allel.opt.model' */ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_ImportError; static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_enumerate; @@ -2766,7 +2771,6 @@ static const char __pyx_k_No_matching_signature_found[] = "No matching signature static const char __pyx_k_genotype_array_pack_diploid[] = "genotype_array_pack_diploid"; static const char __pyx_k_haplotype_array_map_alleles[] = "haplotype_array_map_alleles"; static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static const char __pyx_k_genotype_array_count_alleles[] = "genotype_array_count_alleles"; static const char __pyx_k_genotype_array_unpack_diploid[] = "genotype_array_unpack_diploid"; static const char __pyx_k_haplotype_array_count_alleles[] = "haplotype_array_count_alleles"; @@ -2793,7 +2797,6 @@ static const char __pyx_k_genotype_array_count_alleles_mas[] = "genotype_array_c static const char __pyx_k_genotype_array_count_alleles_sub[] = "genotype_array_count_alleles_subpop"; static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; static const char __pyx_k_haplotype_array_count_alleles_su[] = "haplotype_array_count_alleles_subpop"; -static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; @@ -2908,8 +2911,6 @@ static PyObject *__pyx_n_s_n_samples; static PyObject *__pyx_n_s_n_variants; static PyObject *__pyx_n_s_name; static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; -static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_ndim; static PyObject *__pyx_n_s_new; static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; @@ -3055,8 +3056,6 @@ static PyObject *__pyx_pf_5allel_3opt_5model_172allele_counts_array_map_alleles( static PyObject *__pyx_pf_5allel_3opt_5model_174allele_counts_array_map_alleles(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_ac, __Pyx_memviewslice __pyx_v_mapping, PyObject *__pyx_v_max_allele); /* proto */ static PyObject *__pyx_pf_5allel_3opt_5model_176allele_counts_array_map_alleles(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_ac, __Pyx_memviewslice __pyx_v_mapping, PyObject *__pyx_v_max_allele); /* proto */ static PyObject *__pyx_pf_5allel_3opt_5model_178allele_counts_array_map_alleles(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_ac, __Pyx_memviewslice __pyx_v_mapping, PyObject *__pyx_v_max_allele); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ @@ -3116,7 +3115,7 @@ static PyObject *__pyx_tuple__5; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__8; static PyObject *__pyx_tuple__9; -static PyObject *__pyx_slice__28; +static PyObject *__pyx_slice__26; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; @@ -3133,11 +3132,10 @@ static PyObject *__pyx_tuple__22; static PyObject *__pyx_tuple__23; static PyObject *__pyx_tuple__24; static PyObject *__pyx_tuple__25; -static PyObject *__pyx_tuple__26; static PyObject *__pyx_tuple__27; +static PyObject *__pyx_tuple__28; static PyObject *__pyx_tuple__29; static PyObject *__pyx_tuple__30; -static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__32; static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__36; @@ -3148,12 +3146,12 @@ static PyObject *__pyx_tuple__44; static PyObject *__pyx_tuple__46; static PyObject *__pyx_tuple__48; static PyObject *__pyx_tuple__50; +static PyObject *__pyx_tuple__51; static PyObject *__pyx_tuple__52; static PyObject *__pyx_tuple__53; static PyObject *__pyx_tuple__54; static PyObject *__pyx_tuple__55; -static PyObject *__pyx_tuple__56; -static PyObject *__pyx_tuple__57; +static PyObject *__pyx_codeobj__31; static PyObject *__pyx_codeobj__33; static PyObject *__pyx_codeobj__35; static PyObject *__pyx_codeobj__37; @@ -3163,8 +3161,7 @@ static PyObject *__pyx_codeobj__43; static PyObject *__pyx_codeobj__45; static PyObject *__pyx_codeobj__47; static PyObject *__pyx_codeobj__49; -static PyObject *__pyx_codeobj__51; -static PyObject *__pyx_codeobj__58; +static PyObject *__pyx_codeobj__56; /* Late includes */ /* "allel/opt/model.pyx":25 @@ -3183,6 +3180,9 @@ static PyObject *__pyx_pw_5allel_3opt_5model_1genotype_array_pack_diploid(PyObje PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -3303,6 +3303,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_genotype_array_pack_diploid(CYTHON_ Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("genotype_array_pack_diploid", 0); __Pyx_INCREF(__pyx_v_kwargs); __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 25, __pyx_L1_error) @@ -4002,6 +4005,9 @@ static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5model_21genotype_array_pack_d static PyMethodDef __pyx_fuse_0__pyx_mdef_5allel_3opt_5model_21genotype_array_pack_diploid = {"__pyx_fuse_0genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_0__pyx_pw_5allel_3opt_5model_21genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5model_21genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -4053,11 +4059,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_20genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -4179,10 +4183,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_20genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":50 * @@ -4245,9 +4249,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_20genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -4336,6 +4340,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_23genotype_array_pack_d static PyMethodDef __pyx_fuse_1__pyx_mdef_5allel_3opt_5model_23genotype_array_pack_diploid = {"__pyx_fuse_1genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_1__pyx_pw_5allel_3opt_5model_23genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_23genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -4387,11 +4394,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_22genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -4513,10 +4518,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_22genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":50 * @@ -4579,9 +4584,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_22genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -4670,6 +4675,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_25genotype_array_pack_d static PyMethodDef __pyx_fuse_2__pyx_mdef_5allel_3opt_5model_25genotype_array_pack_diploid = {"__pyx_fuse_2genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_2__pyx_pw_5allel_3opt_5model_25genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_25genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -4721,11 +4729,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_24genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -4847,10 +4853,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_24genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); 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+ int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -5055,11 +5064,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_26genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -5181,10 +5188,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_26genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":50 * @@ -5247,9 +5254,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_26genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -5338,6 +5345,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5model_29genotype_array_pack_d static PyMethodDef __pyx_fuse_4__pyx_mdef_5allel_3opt_5model_29genotype_array_pack_diploid = {"__pyx_fuse_4genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_4__pyx_pw_5allel_3opt_5model_29genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5model_29genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -5389,11 +5399,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_28genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -5515,10 +5523,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_28genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":50 * @@ -5581,9 +5589,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_28genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -5672,6 +5680,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_31genotype_array_pack_d static PyMethodDef __pyx_fuse_5__pyx_mdef_5allel_3opt_5model_31genotype_array_pack_diploid = {"__pyx_fuse_5genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_5__pyx_pw_5allel_3opt_5model_31genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_31genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -5723,11 +5734,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_30genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; 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/* "allel/opt/model.pyx":50 * @@ -5915,9 +5924,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_30genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -6006,6 +6015,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5model_33genotype_array_pack_d static PyMethodDef __pyx_fuse_6__pyx_mdef_5allel_3opt_5model_33genotype_array_pack_diploid = {"__pyx_fuse_6genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_6__pyx_pw_5allel_3opt_5model_33genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5model_33genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -6057,11 +6069,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_32genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -6183,10 +6193,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_32genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_15 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + __pyx_t_12 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_14 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":50 * @@ -6249,9 +6259,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_32genotype_array_pack_diploid(CYTHO * * return np.asarray(packed) */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_18 * __pyx_v_packed.strides[0]) ) + __pyx_t_19 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_packed.data + __pyx_t_12 * __pyx_v_packed.strides[0]) ) + __pyx_t_13 * __pyx_v_packed.strides[1]) )) = __pyx_v_p; } } } @@ -6340,6 +6350,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_35genotype_array_pack_d static PyMethodDef __pyx_fuse_7__pyx_mdef_5allel_3opt_5model_35genotype_array_pack_diploid = {"__pyx_fuse_7genotype_array_pack_diploid", (PyCFunction)__pyx_fuse_7__pyx_pw_5allel_3opt_5model_35genotype_array_pack_diploid, METH_O, 0}; static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_35genotype_array_pack_diploid(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_pack_diploid (wrapper)", 0); @@ -6391,11 +6404,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_34genotype_array_pack_diploid(CYTHO Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7genotype_array_pack_diploid", 0); /* "allel/opt/model.pyx":38 @@ -6517,10 +6528,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_34genotype_array_pack_diploid(CYTHO * * # add 1 to handle missing alleles coded as -1 */ - __pyx_t_15 = __pyx_v_i; 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int __pyx_t_15; - Py_ssize_t __pyx_t_16; - size_t __pyx_t_17; + size_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4haplotype_array_count_alleles", 0); /* "allel/opt/model.pyx":126 @@ -9360,9 +9403,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_46haplotype_array_count_alleles(CYT * * return np.asarray(ac) */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_16 * __pyx_v_ac.strides[0]) ) + __pyx_t_17 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_13 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_13 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":137 * for j in range(n_haplotypes): @@ -9461,6 +9504,9 @@ static PyMethodDef __pyx_fuse_5__pyx_mdef_5allel_3opt_5model_49haplotype_array_c static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_49haplotype_array_count_alleles(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; 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int __pyx_t_15; - Py_ssize_t __pyx_t_16; - size_t __pyx_t_17; + size_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6haplotype_array_count_alleles", 0); /* "allel/opt/model.pyx":126 @@ -10008,9 +10061,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_50haplotype_array_count_alleles(CYT * * return np.asarray(ac) */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_16 * __pyx_v_ac.strides[0]) ) + __pyx_t_17 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_13 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_13 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":137 * for j in range(n_haplotypes): @@ -10109,6 +10162,9 @@ static PyMethodDef __pyx_fuse_7__pyx_mdef_5allel_3opt_5model_53haplotype_array_c static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_53haplotype_array_count_alleles(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint64_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles (wrapper)", 0); @@ -10196,8 +10252,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_52haplotype_array_count_alleles(CYT Py_ssize_t __pyx_t_13; int __pyx_t_14; int __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_uint64_t __pyx_t_17; + __pyx_t_5numpy_uint64_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7haplotype_array_count_alleles", 0); /* "allel/opt/model.pyx":126 @@ -10332,9 +10390,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_52haplotype_array_count_alleles(CYT * * return np.asarray(ac) */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_16 * __pyx_v_ac.strides[0]) ) + __pyx_t_17 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_13 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_13 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":137 * for j in range(n_haplotypes): @@ -10443,6 +10501,9 @@ static PyObject *__pyx_pw_5allel_3opt_5model_7haplotype_array_count_alleles_subp PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -10563,6 +10624,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_6haplotype_array_count_alleles_subp Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop", 0); 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+ int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -11487,9 +11555,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_56haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_v_allele = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_13 * __pyx_v_h.strides[0]) ) + __pyx_t_14 * __pyx_v_h.strides[1]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_v_allele = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_12 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -11498,12 +11566,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_56haplotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -11512,9 +11580,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_56haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -11615,6 +11683,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_59haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int16_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -11713,12 +11784,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_58haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + Py_ssize_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -11838,9 +11910,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_58haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; 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- __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -11966,6 +12038,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_61haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int32_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -12064,12 +12139,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_60haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + Py_ssize_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -12189,9 +12265,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_60haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_13 * __pyx_v_h.strides[0]) ) + __pyx_t_14 * __pyx_v_h.strides[1]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_12 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -12200,12 +12276,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_60haplotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -12214,9 +12290,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_60haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -12317,6 +12393,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5model_63haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -12415,12 +12494,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_62haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - __pyx_t_5numpy_int64_t __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; 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+ __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -12565,9 +12644,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_62haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_13 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -12668,6 +12747,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5model_65haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint8_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -12766,12 +12848,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_64haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - size_t __pyx_t_18; + size_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -12891,9 +12974,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_64haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_13 * __pyx_v_h.strides[0]) ) + __pyx_t_14 * __pyx_v_h.strides[1]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_12 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -12902,12 +12985,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_64haplotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -12916,9 +12999,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_64haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -13019,6 +13102,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_67haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint16_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -13117,12 +13203,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_66haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - size_t __pyx_t_18; + size_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -13242,9 +13329,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_66haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_13 * __pyx_v_h.strides[0]) ) + __pyx_t_14 * __pyx_v_h.strides[1]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_12 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -13253,12 +13340,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_66haplotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -13267,9 +13354,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_66haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -13370,6 +13457,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5model_69haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint32_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -13468,12 +13558,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_68haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - size_t __pyx_t_18; + size_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; 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+ __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_16 = (__pyx_t_15 != 0); - if (__pyx_t_16) { + __pyx_t_15 = (__pyx_t_14 != 0); + if (__pyx_t_15) { /* "allel/opt/model.pyx":168 * allele = h[i, idx] @@ -13618,9 +13709,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_68haplotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_18 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_12 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":167 * idx = subpop[j] @@ -13721,6 +13812,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_71haplotype_array_count __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("haplotype_array_count_alleles_subpop (wrapper)", 0); @@ -13819,12 +13913,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_70haplotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; int __pyx_t_15; - int __pyx_t_16; - Py_ssize_t __pyx_t_17; - __pyx_t_5numpy_uint64_t __pyx_t_18; + __pyx_t_5numpy_uint64_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7haplotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":155 @@ -13944,9 +14039,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_70haplotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_13 = __pyx_v_i; 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int __pyx_t_19; - Py_ssize_t __pyx_t_20; - Py_ssize_t __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0genotype_array_count_alleles", 0); /* "allel/opt/model.pyx":183 @@ -15152,9 +15257,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_74genotype_array_count_alleles(CYTH * * return np.asarray(ac) */ - __pyx_t_20 = __pyx_v_i; - __pyx_t_21 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_20 * __pyx_v_ac.strides[0]) ) + __pyx_t_21 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_16 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_16 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":197 * for k in range(ploidy): @@ -15254,6 +15359,9 @@ static PyMethodDef __pyx_fuse_1__pyx_mdef_5allel_3opt_5model_77genotype_array_co static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_77genotype_array_count_alleles(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; 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} - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -18834,9 +18980,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_92genotype_array_count_alleles_mask * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_22 * __pyx_v_ac.strides[0]) ) + __pyx_t_23 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -18947,6 +19093,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_95genotype_array_count_ __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int16_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_masked (wrapper)", 0); @@ -19052,11 +19201,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_94genotype_array_count_alleles_mask Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -19199,10 +19347,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_94genotype_array_count_alleles_mask * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - __pyx_t_20 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_19 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); + __pyx_t_13 = __pyx_v_i; + __pyx_t_12 = __pyx_v_j; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_12 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -19215,8 +19363,8 @@ static PyObject *__pyx_pf_5allel_3opt_5model_94genotype_array_count_alleles_mask if (__pyx_t_14) { __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -19225,9 +19373,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_94genotype_array_count_alleles_mask * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_22 * __pyx_v_ac.strides[0]) ) + __pyx_t_23 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -19338,6 +19486,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_97genotype_array_count_ __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int32_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_masked (wrapper)", 0); @@ -19443,11 +19594,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_96genotype_array_count_alleles_mask Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -19590,10 +19740,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_96genotype_array_count_alleles_mask * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - __pyx_t_20 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_19 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); + __pyx_t_13 = __pyx_v_i; + __pyx_t_12 = __pyx_v_j; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_12 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -19606,8 +19756,8 @@ static PyObject *__pyx_pf_5allel_3opt_5model_96genotype_array_count_alleles_mask if (__pyx_t_14) { __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -19616,9 +19766,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_96genotype_array_count_alleles_mask * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_22 * __pyx_v_ac.strides[0]) ) + __pyx_t_23 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -19729,6 +19879,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5model_99genotype_array_count_ __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int64_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_masked (wrapper)", 0); @@ -19834,11 +19987,11 @@ static PyObject *__pyx_pf_5allel_3opt_5model_98genotype_array_count_alleles_mask Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - __pyx_t_5numpy_int64_t __pyx_t_23; + int __pyx_t_19; + __pyx_t_5numpy_int64_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -19981,10 +20134,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_98genotype_array_count_alleles_mask * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - __pyx_t_20 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_19 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); + __pyx_t_13 = __pyx_v_i; + __pyx_t_12 = __pyx_v_j; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_12 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -19997,8 +20150,8 @@ static PyObject *__pyx_pf_5allel_3opt_5model_98genotype_array_count_alleles_mask if (__pyx_t_14) { __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -20007,9 +20160,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_98genotype_array_count_alleles_mask * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; 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Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - size_t __pyx_t_23; + int __pyx_t_19; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -20372,10 +20528,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_100genotype_array_count_alleles_mas * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - __pyx_t_20 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_19 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); + __pyx_t_13 = __pyx_v_i; + __pyx_t_12 = __pyx_v_j; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_12 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -20388,8 +20544,8 @@ static PyObject *__pyx_pf_5allel_3opt_5model_100genotype_array_count_alleles_mas if (__pyx_t_14) { __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -20398,9 +20554,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_100genotype_array_count_alleles_mas * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_22 * __pyx_v_ac.strides[0]) ) + __pyx_t_23 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -20511,6 +20667,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_103genotype_array_count __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint16_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_masked (wrapper)", 0); @@ -20616,11 +20775,11 @@ static PyObject *__pyx_pf_5allel_3opt_5model_102genotype_array_count_alleles_mas Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - size_t __pyx_t_23; + int __pyx_t_19; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -20763,10 +20922,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_102genotype_array_count_alleles_mas * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_j; - __pyx_t_20 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_19 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); + __pyx_t_13 = __pyx_v_i; + __pyx_t_12 = __pyx_v_j; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_12 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":230 * for k in range(ploidy): @@ -20779,8 +20938,8 @@ static PyObject *__pyx_pf_5allel_3opt_5model_102genotype_array_count_alleles_mas if (__pyx_t_14) { __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_21 = (__pyx_t_14 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":231 * allele = g[i, j, k] @@ -20789,9 +20948,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_102genotype_array_count_alleles_mas * * return np.asarray(ac) */ - __pyx_t_22 = __pyx_v_i; 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__Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint64_t __pyx_v_max_allele; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_masked (wrapper)", 0); @@ -21398,11 +21563,11 @@ static PyObject *__pyx_pf_5allel_3opt_5model_106genotype_array_count_alleles_mas Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - Py_ssize_t __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - __pyx_t_5numpy_uint64_t __pyx_t_23; + int __pyx_t_19; + __pyx_t_5numpy_uint64_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7genotype_array_count_alleles_masked", 0); /* "allel/opt/model.pyx":214 @@ -21545,10 +21710,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_106genotype_array_count_alleles_mas * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_18 = __pyx_v_i; 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- __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - Py_ssize_t __pyx_t_22; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -22764,10 +22938,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_110genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_idx; - __pyx_t_18 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_idx; + __pyx_t_17 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); 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- if (__pyx_t_19) { - __pyx_t_19 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_18 = (0 <= __pyx_v_allele); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_20 = (__pyx_t_19 != 0); - if (__pyx_t_20) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":263 * allele = g[i, idx, k] @@ -23170,9 +23347,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_112genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_21 = __pyx_v_i; - __pyx_t_22 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_21 * __pyx_v_ac.strides[0]) ) + __pyx_t_22 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":262 * for k in range(ploidy): @@ -23274,6 +23451,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_115genotype_array_count __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int32_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -23377,13 +23557,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_114genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - Py_ssize_t __pyx_t_22; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -23524,10 +23704,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_114genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; 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} - __pyx_t_20 = (__pyx_t_19 != 0); - if (__pyx_t_20) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":263 * allele = g[i, idx, k] @@ -23550,9 +23730,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_114genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_21 = __pyx_v_i; - __pyx_t_22 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_21 * __pyx_v_ac.strides[0]) ) + __pyx_t_22 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":262 * for k in range(ploidy): @@ -23654,6 +23834,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5model_117genotype_array_count __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -23757,13 +23940,13 @@ static PyObject *__pyx_pf_5allel_3opt_5model_116genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - __pyx_t_5numpy_int64_t __pyx_t_22; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -23904,10 +24087,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_116genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; 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__Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -24137,13 +24323,14 @@ static PyObject *__pyx_pf_5allel_3opt_5model_118genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - size_t __pyx_t_22; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -24284,10 +24471,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_118genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; 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__Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -24517,13 +24707,14 @@ static PyObject *__pyx_pf_5allel_3opt_5model_120genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - size_t __pyx_t_22; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -24664,10 +24855,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_120genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; 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__Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -24897,13 +25091,14 @@ static PyObject *__pyx_pf_5allel_3opt_5model_122genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - size_t __pyx_t_22; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -25044,10 +25239,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_122genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_idx; - __pyx_t_18 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_16 = __pyx_v_idx; + __pyx_t_17 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_16 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":262 * for k in range(ploidy): @@ -25056,12 +25251,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_122genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_19 = (0 <= __pyx_v_allele); - if (__pyx_t_19) { - __pyx_t_19 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_18 = (0 <= __pyx_v_allele); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_20 = (__pyx_t_19 != 0); - if (__pyx_t_20) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":263 * allele = g[i, idx, k] @@ -25070,9 +25265,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_122genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_21 = __pyx_v_i; - __pyx_t_22 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_21 * __pyx_v_ac.strides[0]) ) + __pyx_t_22 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":262 * for k in range(ploidy): @@ -25174,6 +25369,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_125genotype_array_count __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop (wrapper)", 0); @@ -25277,13 +25475,14 @@ static PyObject *__pyx_pf_5allel_3opt_5model_124genotype_array_count_alleles_sub Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - __pyx_t_5numpy_int64_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + __pyx_t_5numpy_int64_t __pyx_t_16; + Py_ssize_t __pyx_t_17; + int __pyx_t_18; int __pyx_t_19; - int __pyx_t_20; - Py_ssize_t __pyx_t_21; - __pyx_t_5numpy_uint64_t __pyx_t_22; + __pyx_t_5numpy_uint64_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7genotype_array_count_alleles_subpop", 0); /* "allel/opt/model.pyx":248 @@ -25424,10 +25623,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_124genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_16 = __pyx_v_i; 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} - __pyx_t_20 = (__pyx_t_19 != 0); - if (__pyx_t_20) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":263 * allele = g[i, idx, k] @@ -25450,9 +25649,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_124genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_21 = __pyx_v_i; - __pyx_t_22 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_21 * __pyx_v_ac.strides[0]) ) + __pyx_t_22 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_17 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":262 * for k in range(ploidy): @@ -25563,6 +25762,9 @@ static PyObject *__pyx_pw_5allel_3opt_5model_15genotype_array_count_alleles_subp PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; 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- if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -26688,9 +26894,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_128genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -26803,6 +27009,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5model_131genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int16_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -26916,18 +27125,16 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -27056,10 +27263,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -27068,10 +27275,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -27080,10 +27287,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -27092,12 +27299,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -27106,9 +27313,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_130genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -27221,6 +27428,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5model_133genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int32_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -27334,18 +27544,16 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -27474,10 +27682,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -27486,10 +27694,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -27498,10 +27706,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -27510,12 +27718,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -27524,9 +27732,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_132genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_12 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_12 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -27639,6 +27847,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5model_135genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_int64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -27752,18 +27963,16 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_int64_t __pyx_t_24; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -27892,10 +28101,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -27904,10 +28113,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -27916,10 +28125,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -27928,12 +28137,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -27942,9 +28151,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_134genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_13 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_13 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -28057,6 +28266,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5model_137genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint8_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -28170,18 +28382,17 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - size_t __pyx_t_24; + int __pyx_t_19; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -28310,10 +28521,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -28322,10 +28533,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -28334,10 +28545,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -28346,12 +28557,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -28360,9 +28571,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_136genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -28475,6 +28686,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5model_139genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint16_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -28588,18 +28802,17 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - size_t __pyx_t_24; + int __pyx_t_19; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -28728,10 +28941,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -28740,10 +28953,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -28752,10 +28965,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -28764,12 +28977,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -28778,9 +28991,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_138genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -28893,6 +29106,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5model_141genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint32_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -29006,18 +29222,17 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - size_t __pyx_t_24; + int __pyx_t_19; + size_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -29146,10 +29361,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); - if (__pyx_t_15) { + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_14 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_12 * __pyx_v_mask.strides[0]) ) + __pyx_t_13 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); + if (__pyx_t_14) { /* "allel/opt/model.pyx":295 * # deal with mask @@ -29158,10 +29373,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub * allele = g[i, idx, k] * if 0 <= allele <= max_allele: */ - __pyx_t_16 = __pyx_v_ploidy; - __pyx_t_17 = __pyx_t_16; - for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { - __pyx_v_k = __pyx_t_18; + __pyx_t_15 = __pyx_v_ploidy; + __pyx_t_16 = __pyx_t_15; + for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { + __pyx_v_k = __pyx_t_17; /* "allel/opt/model.pyx":296 * if not mask[i, idx]: @@ -29170,10 +29385,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub * if 0 <= allele <= max_allele: * ac[i, allele] += 1 */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_idx; - __pyx_t_21 = __pyx_v_k; - __pyx_v_allele = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_idx; + __pyx_t_18 = __pyx_v_k; + __pyx_v_allele = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_13 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -29182,12 +29397,12 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub * ac[i, allele] += 1 * */ - __pyx_t_15 = (0 <= __pyx_v_allele); - if (__pyx_t_15) { - __pyx_t_15 = (__pyx_v_allele <= __pyx_v_max_allele); + __pyx_t_14 = (0 <= __pyx_v_allele); + if (__pyx_t_14) { + __pyx_t_14 = (__pyx_v_allele <= __pyx_v_max_allele); } - __pyx_t_22 = (__pyx_t_15 != 0); - if (__pyx_t_22) { + __pyx_t_19 = (__pyx_t_14 != 0); + if (__pyx_t_19) { /* "allel/opt/model.pyx":298 * allele = g[i, idx, k] @@ -29196,9 +29411,9 @@ static PyObject *__pyx_pf_5allel_3opt_5model_140genotype_array_count_alleles_sub * * return np.asarray(ac) */ - __pyx_t_23 = __pyx_v_i; - __pyx_t_24 = __pyx_v_allele; - *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_23 * __pyx_v_ac.strides[0]) ) + __pyx_t_24 * __pyx_v_ac.strides[1]) )) += 1; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_allele; + *((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ac.data + __pyx_t_18 * __pyx_v_ac.strides[0]) ) + __pyx_t_20 * __pyx_v_ac.strides[1]) )) += 1; /* "allel/opt/model.pyx":297 * for k in range(ploidy): @@ -29311,6 +29526,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5model_143genotype_array_count __Pyx_memviewslice __pyx_v_mask = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_uint64_t __pyx_v_max_allele; __Pyx_memviewslice __pyx_v_subpop = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("genotype_array_count_alleles_subpop_masked (wrapper)", 0); @@ -29424,18 +29642,17 @@ static PyObject *__pyx_pf_5allel_3opt_5model_142genotype_array_count_alleles_sub Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - __pyx_t_5numpy_int64_t __pyx_t_14; - int __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_13; + int __pyx_t_14; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - __pyx_t_5numpy_int64_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - int __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_uint64_t __pyx_t_24; + int __pyx_t_19; + __pyx_t_5numpy_uint64_t __pyx_t_20; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7genotype_array_count_alleles_subpop_masked", 0); /* "allel/opt/model.pyx":281 @@ -29564,10 +29781,10 @@ static PyObject *__pyx_pf_5allel_3opt_5model_142genotype_array_count_alleles_sub * for k in range(ploidy): * allele = g[i, idx, k] */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = __pyx_v_idx; - __pyx_t_15 = ((!((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mask.data + __pyx_t_13 * __pyx_v_mask.strides[0]) ) + __pyx_t_14 * __pyx_v_mask.strides[1]) ))) != 0)) != 0); 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__Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__setstate_cython__", 0); /* "(tree fragment)":17 @@ -42962,6 +42484,9 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar PyObject *__pyx_v_obj = 0; int __pyx_v_flags; int __pyx_v_dtype_is_object; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); @@ -43042,6 +42567,9 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); /* "View.MemoryView":346 @@ -43357,7 +42885,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal * def __dealloc__(memoryview self): * if self.obj is not None: # <<<<<<<<<<<<<< * __Pyx_ReleaseBuffer(&self.view) - * + * elif (<__pyx_buffer *> &self.view).obj == Py_None: */ __pyx_t_1 = (__pyx_v_self->obj != Py_None); 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+ + /* "View.MemoryView":378 + * + * (<__pyx_buffer *> &self.view).obj = NULL + * Py_DECREF(Py_None) # <<<<<<<<<<<<<< + * + * cdef int i + */ + Py_DECREF(Py_None); + + /* "View.MemoryView":375 + * if self.obj is not None: + * __Pyx_ReleaseBuffer(&self.view) + * elif (<__pyx_buffer *> &self.view).obj == Py_None: # <<<<<<<<<<<<<< * + * (<__pyx_buffer *> &self.view).obj = NULL */ } + __pyx_L3:; - /* "View.MemoryView":378 + /* "View.MemoryView":382 * cdef int i * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: # <<<<<<<<<<<<<< @@ -43391,7 +42958,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_self->lock != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":379 + /* "View.MemoryView":383 * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): # <<<<<<<<<<<<<< @@ -43403,7 +42970,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -43413,7 +42980,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = (((__pyx_memoryview_thread_locks[__pyx_v_i]) == __pyx_v_self->lock) != 0); if (__pyx_t_2) { - /* "View.MemoryView":381 + /* "View.MemoryView":385 * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 # <<<<<<<<<<<<<< @@ -43422,7 +42989,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ __pyx_memoryview_thread_locks_used = (__pyx_memoryview_thread_locks_used - 1); - /* "View.MemoryView":382 + /* "View.MemoryView":386 * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: # <<<<<<<<<<<<<< @@ -43432,7 +42999,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_i != __pyx_memoryview_thread_locks_used) != 0); if (__pyx_t_2) { - /* "View.MemoryView":384 + /* "View.MemoryView":388 * if i != __pyx_memoryview_thread_locks_used: * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( * __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i]) # <<<<<<<<<<<<<< @@ -43442,7 +43009,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_6 = (__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]); __pyx_t_7 = (__pyx_memoryview_thread_locks[__pyx_v_i]); - /* "View.MemoryView":383 + /* "View.MemoryView":387 * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( # <<<<<<<<<<<<<< @@ -43452,7 +43019,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal (__pyx_memoryview_thread_locks[__pyx_v_i]) = __pyx_t_6; (__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]) = __pyx_t_7; - /* "View.MemoryView":382 + /* "View.MemoryView":386 * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: # <<<<<<<<<<<<<< @@ -43461,7 +43028,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ } - /* "View.MemoryView":385 + /* "View.MemoryView":389 * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( * __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i]) * break # <<<<<<<<<<<<<< @@ -43470,7 +43037,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ goto __pyx_L6_break; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -43481,7 +43048,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } /*else*/ { - /* "View.MemoryView":387 + /* "View.MemoryView":391 * break * else: * PyThread_free_lock(self.lock) # <<<<<<<<<<<<<< @@ -43492,7 +43059,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } __pyx_L6_break:; 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__pyx_v_info->shape = __pyx_t_4; - /* "View.MemoryView":518 + /* "View.MemoryView":522 * raise ValueError("Cannot create writable memory view from read-only memoryview") * * if flags & PyBUF_ND: # <<<<<<<<<<<<<< @@ -45312,7 +44915,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu goto __pyx_L6; } - /* "View.MemoryView":521 + /* "View.MemoryView":525 * info.shape = self.view.shape * else: * info.shape = NULL # <<<<<<<<<<<<<< @@ -45324,7 +44927,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu } __pyx_L6:; - /* "View.MemoryView":523 + /* "View.MemoryView":527 * info.shape = NULL * * if flags & PyBUF_STRIDES: # <<<<<<<<<<<<<< @@ -45334,7 +44937,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_STRIDES) != 0); if (__pyx_t_1) { - /* "View.MemoryView":524 + /* "View.MemoryView":528 * * if flags & PyBUF_STRIDES: * info.strides = self.view.strides # <<<<<<<<<<<<<< @@ -45344,7 +44947,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_4 = __pyx_v_self->view.strides; 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if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 744, __pyx_L1_error) + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_t_10, 0, 0, 0, 0, 0, 0); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 748, __pyx_L1_error) - /* "View.MemoryView":743 + /* "View.MemoryView":747 * * for dim, index in enumerate(indices): * if PyIndex_Check(index): # <<<<<<<<<<<<<< @@ -47932,7 +47599,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ goto __pyx_L6; } - /* "View.MemoryView":750 + /* "View.MemoryView":754 * 0, 0, 0, # have_{start,stop,step} * False) * elif index is None: # <<<<<<<<<<<<<< @@ -47943,7 +47610,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_1 = (__pyx_t_2 != 0); if (__pyx_t_1) { - /* "View.MemoryView":751 + /* "View.MemoryView":755 * False) * elif index is None: * p_dst.shape[new_ndim] = 1 # <<<<<<<<<<<<<< @@ -47952,7 +47619,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ (__pyx_v_p_dst->shape[__pyx_v_new_ndim]) = 1; 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- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(2, 758, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(2, 762, __pyx_L1_error) if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 758, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 762, __pyx_L1_error) __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L11_bool_binop_done; @@ -48056,55 +47723,55 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L11_bool_binop_done:; __pyx_v_step = __pyx_t_10; - /* "View.MemoryView":760 + /* "View.MemoryView":764 * step = index.step or 0 * * have_start = index.start is not None # <<<<<<<<<<<<<< * have_stop = index.stop is not None * have_step = index.step is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 760, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 764, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_start = __pyx_t_1; - /* "View.MemoryView":761 + /* "View.MemoryView":765 * * have_start = index.start is not None * have_stop = index.stop is not None # <<<<<<<<<<<<<< * have_step = index.step is not None * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 761, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 765, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_stop = __pyx_t_1; - /* "View.MemoryView":762 + /* "View.MemoryView":766 * have_start = index.start is not None * have_stop = index.stop is not None * have_step = index.step is not None # <<<<<<<<<<<<<< * * slice_memviewslice( */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 762, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 766, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_step = __pyx_t_1; - /* "View.MemoryView":764 + /* "View.MemoryView":768 * have_step = index.step is not None * * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 764, __pyx_L1_error) + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 768, __pyx_L1_error) - /* "View.MemoryView":770 + /* "View.MemoryView":774 * have_start, have_stop, have_step, * True) * new_ndim += 1 # <<<<<<<<<<<<<< @@ -48115,7 +47782,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L6:; - /* "View.MemoryView":742 + /* "View.MemoryView":746 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -48125,7 +47792,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -48136,7 +47803,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< @@ -48145,39 +47812,39 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":774 + /* "View.MemoryView":778 * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, # <<<<<<<<<<<<<< * memviewsliceobj.to_dtype_func, * memview.dtype_is_object) */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 774, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 778, __pyx_L1_error) } - /* "View.MemoryView":775 + /* "View.MemoryView":779 * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, # <<<<<<<<<<<<<< * memview.dtype_is_object) * else: */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 775, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 779, __pyx_L1_error) } - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 773, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 777, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 773, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 777, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -48186,7 +47853,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ } - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< @@ -48196,30 +47863,30 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ /*else*/ { __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":779 + /* "View.MemoryView":783 * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 778, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 782, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 778, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 782, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":706 + /* "View.MemoryView":710 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -48241,7 +47908,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ return __pyx_r; } -/* "View.MemoryView":803 +/* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -48256,8 +47923,11 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, int __pyx_t_1; int __pyx_t_2; int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -48267,7 +47937,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -48277,7 +47947,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((__pyx_v_start < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":826 + /* "View.MemoryView":830 * * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -48286,7 +47956,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -48295,7 +47965,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -48309,16 +47979,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":828 + /* "View.MemoryView":832 * start += shape * if not 0 <= start < shape: * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< * else: * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 828, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 832, __pyx_L1_error) - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -48327,7 +47997,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -48337,7 +48007,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L3; } - /* "View.MemoryView":831 + /* "View.MemoryView":835 * else: * * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< @@ -48356,7 +48026,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L6_bool_binop_done:; __pyx_v_negative_step = __pyx_t_2; - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -48374,16 +48044,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L9_bool_binop_done:; if (__pyx_t_2) { - /* "View.MemoryView":834 + /* "View.MemoryView":838 * * if have_step and step == 0: * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 834, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 838, __pyx_L1_error) - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -48392,7 +48062,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -48402,7 +48072,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_start != 0); if (__pyx_t_2) { - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -48412,7 +48082,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":839 + /* "View.MemoryView":843 * if have_start: * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -48421,7 +48091,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -48431,7 +48101,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":841 + /* "View.MemoryView":845 * start += shape * if start < 0: * start = 0 # <<<<<<<<<<<<<< @@ -48440,7 +48110,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = 0; - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -48449,7 +48119,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -48459,7 +48129,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L12; } - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -48469,7 +48139,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -48479,7 +48149,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":844 + /* "View.MemoryView":848 * elif start >= shape: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -48488,7 +48158,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -48498,7 +48168,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L14; } - /* "View.MemoryView":846 + /* "View.MemoryView":850 * start = shape - 1 * else: * start = shape # <<<<<<<<<<<<<< @@ -48510,7 +48180,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L14:; - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -48520,7 +48190,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L12:; - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -48530,7 +48200,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L11; } - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -48541,7 +48211,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":849 + /* "View.MemoryView":853 * else: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -48550,7 +48220,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -48560,7 +48230,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L15; } - /* "View.MemoryView":851 + /* "View.MemoryView":855 * start = shape - 1 * else: * start = 0 # <<<<<<<<<<<<<< @@ -48574,7 +48244,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L11:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -48584,7 +48254,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_stop != 0); if (__pyx_t_2) { - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -48594,7 +48264,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":855 + /* "View.MemoryView":859 * if have_stop: * if stop < 0: * stop += shape # <<<<<<<<<<<<<< @@ -48603,7 +48273,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -48613,7 +48283,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":857 + /* "View.MemoryView":861 * stop += shape * if stop < 0: * stop = 0 # <<<<<<<<<<<<<< @@ -48622,7 +48292,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = 0; - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -48631,7 +48301,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -48641,7 +48311,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L17; } - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -48651,7 +48321,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":859 + /* "View.MemoryView":863 * stop = 0 * elif stop > shape: * stop = shape # <<<<<<<<<<<<<< @@ -48660,7 +48330,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = __pyx_v_shape; - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -48670,7 +48340,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L17:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -48680,7 +48350,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L16; } - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -48691,7 +48361,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":862 + /* "View.MemoryView":866 * else: * if negative_step: * stop = -1 # <<<<<<<<<<<<<< @@ -48700,7 +48370,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = -1L; - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -48710,7 +48380,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L19; } - /* "View.MemoryView":864 + /* "View.MemoryView":868 * stop = -1 * else: * stop = shape # <<<<<<<<<<<<<< @@ -48724,7 +48394,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L16:; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -48734,7 +48404,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":867 + /* "View.MemoryView":871 * * if not have_step: * step = 1 # <<<<<<<<<<<<<< @@ -48743,7 +48413,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_step = 1; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -48752,7 +48422,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":871 + /* "View.MemoryView":875 * * with cython.cdivision(True): * new_shape = (stop - start) // step # <<<<<<<<<<<<<< @@ -48761,7 +48431,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -48771,7 +48441,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":874 + /* "View.MemoryView":878 * * if (stop - start) - step * new_shape: * new_shape += 1 # <<<<<<<<<<<<<< @@ -48780,7 +48450,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = (__pyx_v_new_shape + 1); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -48789,7 +48459,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -48799,7 +48469,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":877 + /* "View.MemoryView":881 * * if new_shape < 0: * new_shape = 0 # <<<<<<<<<<<<<< @@ -48808,7 +48478,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = 0; - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -48817,7 +48487,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":880 + /* "View.MemoryView":884 * * * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< @@ -48826,7 +48496,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - /* "View.MemoryView":881 + /* "View.MemoryView":885 * * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< @@ -48835,7 +48505,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - /* "View.MemoryView":882 + /* "View.MemoryView":886 * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< @@ -48846,7 +48516,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L3:; - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -48856,7 +48526,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":886 + /* "View.MemoryView":890 * * if suboffset_dim[0] < 0: * dst.data += start * stride # <<<<<<<<<<<<<< @@ -48865,7 +48535,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -48875,7 +48545,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L23; } - /* "View.MemoryView":888 + /* "View.MemoryView":892 * dst.data += start * stride * else: * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< @@ -48888,7 +48558,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L23:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -48898,7 +48568,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -48908,7 +48578,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -48918,7 +48588,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":893 + /* "View.MemoryView":897 * if not is_slice: * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< @@ -48927,7 +48597,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -48937,7 +48607,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L26; } - /* "View.MemoryView":895 + /* "View.MemoryView":899 * dst.data = ( dst.data)[0] + suboffset * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< @@ -48946,18 +48616,18 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ /*else*/ { - /* "View.MemoryView":896 + /* "View.MemoryView":900 * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< * else: * suboffset_dim[0] = new_ndim */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 895, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 899, __pyx_L1_error) } __pyx_L26:; - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -48967,7 +48637,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L25; } - /* "View.MemoryView":898 + /* "View.MemoryView":902 * "must be indexed and not sliced", dim) * else: * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< @@ -48979,7 +48649,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L25:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -48988,7 +48658,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":900 + /* "View.MemoryView":904 * suboffset_dim[0] = new_ndim * * return 0 # <<<<<<<<<<<<<< @@ -48998,7 +48668,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":803 + /* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -49022,7 +48692,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, return __pyx_r; } -/* "View.MemoryView":906 +/* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -49042,9 +48712,12 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("pybuffer_index", 0); - /* "View.MemoryView":908 + /* "View.MemoryView":912 * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< @@ -49053,7 +48726,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_suboffset = -1L; - /* "View.MemoryView":909 + /* "View.MemoryView":913 * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 * cdef Py_ssize_t itemsize = view.itemsize # <<<<<<<<<<<<<< @@ -49063,7 +48736,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_1 = __pyx_v_view->itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":912 + /* "View.MemoryView":916 * cdef char *resultp * * if view.ndim == 0: # <<<<<<<<<<<<<< @@ -49073,7 +48746,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":913 + /* "View.MemoryView":917 * * if view.ndim == 0: * shape = view.len / itemsize # <<<<<<<<<<<<<< @@ -49082,15 +48755,15 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ if (unlikely(__pyx_v_itemsize == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); 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} - /* "View.MemoryView":916 + /* "View.MemoryView":920 * stride = itemsize * else: * shape = view.shape[dim] # <<<<<<<<<<<<<< @@ -49119,7 +48792,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P /*else*/ { __pyx_v_shape = (__pyx_v_view->shape[__pyx_v_dim]); - /* "View.MemoryView":917 + /* "View.MemoryView":921 * else: * shape = view.shape[dim] * stride = view.strides[dim] # <<<<<<<<<<<<<< @@ -49128,7 +48801,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_stride = (__pyx_v_view->strides[__pyx_v_dim]); - /* "View.MemoryView":918 + /* "View.MemoryView":922 * shape = view.shape[dim] * stride = view.strides[dim] * if view.suboffsets != NULL: # <<<<<<<<<<<<<< @@ -49138,7 +48811,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->suboffsets != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":919 + /* "View.MemoryView":923 * stride = view.strides[dim] * if view.suboffsets != NULL: * suboffset = view.suboffsets[dim] # <<<<<<<<<<<<<< @@ -49147,7 +48820,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_suboffset = (__pyx_v_view->suboffsets[__pyx_v_dim]); 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if (unlikely(__pyx_t_2)) { - /* "View.MemoryView":924 + /* "View.MemoryView":928 * index += view.shape[dim] * if index < 0: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * if index >= shape: */ - __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 928, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 928, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 928, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __PYX_ERR(2, 924, __pyx_L1_error) + __PYX_ERR(2, 928, __pyx_L1_error) - /* "View.MemoryView":923 + /* "View.MemoryView":927 * if index < 0: * index += view.shape[dim] * if index < 0: # <<<<<<<<<<<<<< @@ -49215,7 +48888,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":921 + /* "View.MemoryView":925 * suboffset = view.suboffsets[dim] * * if index < 0: # <<<<<<<<<<<<<< @@ -49224,7 +48897,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":926 + /* "View.MemoryView":930 * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) * * if index >= shape: # <<<<<<<<<<<<<< @@ -49234,26 +48907,26 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index >= __pyx_v_shape) != 0); if (unlikely(__pyx_t_2)) { - /* "View.MemoryView":927 + /* "View.MemoryView":931 * * if index >= shape: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * resultp = bufp + index * stride */ - __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 931, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 931, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 931, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __PYX_ERR(2, 927, __pyx_L1_error) + __PYX_ERR(2, 931, __pyx_L1_error) - /* "View.MemoryView":926 + /* "View.MemoryView":930 * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) * * if index >= shape: # <<<<<<<<<<<<<< @@ -49262,7 +48935,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":929 + /* "View.MemoryView":933 * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) * * resultp = bufp + index * stride # <<<<<<<<<<<<<< @@ -49271,7 +48944,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_resultp = (__pyx_v_bufp + (__pyx_v_index * __pyx_v_stride)); - /* "View.MemoryView":930 + /* "View.MemoryView":934 * * resultp = bufp + index * stride * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -49281,7 +48954,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":931 + /* "View.MemoryView":935 * resultp = bufp + index * stride * if suboffset >= 0: * resultp = ( resultp)[0] + suboffset # <<<<<<<<<<<<<< @@ -49290,7 +48963,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":930 + /* "View.MemoryView":934 * * resultp = bufp + index * stride * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -49299,7 +48972,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":933 + /* "View.MemoryView":937 * resultp = ( resultp)[0] + suboffset * * return resultp # <<<<<<<<<<<<<< @@ -49309,7 +48982,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_r = __pyx_v_resultp; goto __pyx_L0; - /* "View.MemoryView":906 + /* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -49328,7 +49001,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P return __pyx_r; } -/* "View.MemoryView":939 +/* "View.MemoryView":943 * * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: # <<<<<<<<<<<<<< @@ -49352,8 +49025,11 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { int __pyx_t_7; int __pyx_t_8; int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; - /* "View.MemoryView":940 + /* "View.MemoryView":944 * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: * cdef int ndim = memslice.memview.view.ndim # <<<<<<<<<<<<<< @@ -49363,7 +49039,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_1 = __pyx_v_memslice->memview->view.ndim; __pyx_v_ndim = __pyx_t_1; - /* "View.MemoryView":942 + /* "View.MemoryView":946 * cdef int ndim = memslice.memview.view.ndim * * cdef Py_ssize_t *shape = memslice.shape # <<<<<<<<<<<<<< @@ -49373,7 +49049,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_2 = __pyx_v_memslice->shape; __pyx_v_shape = __pyx_t_2; - /* "View.MemoryView":943 + /* "View.MemoryView":947 * * cdef Py_ssize_t *shape = memslice.shape * cdef Py_ssize_t *strides = memslice.strides # <<<<<<<<<<<<<< @@ -49383,7 +49059,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_2 = __pyx_v_memslice->strides; __pyx_v_strides = __pyx_t_2; - /* "View.MemoryView":947 + /* "View.MemoryView":951 * * cdef int i, j * for i in range(ndim / 2): # <<<<<<<<<<<<<< @@ -49395,7 +49071,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_4; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":948 + /* "View.MemoryView":952 * cdef int i, j * for i in range(ndim / 2): * j = ndim - 1 - i # <<<<<<<<<<<<<< @@ -49404,7 +49080,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { */ __pyx_v_j = ((__pyx_v_ndim - 1) - __pyx_v_i); - /* "View.MemoryView":949 + /* "View.MemoryView":953 * for i in range(ndim / 2): * j = ndim - 1 - i * strides[i], strides[j] = strides[j], strides[i] # <<<<<<<<<<<<<< @@ -49416,7 +49092,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { (__pyx_v_strides[__pyx_v_i]) = __pyx_t_5; (__pyx_v_strides[__pyx_v_j]) = __pyx_t_6; - /* "View.MemoryView":950 + /* "View.MemoryView":954 * j = ndim - 1 - i * strides[i], strides[j] = strides[j], strides[i] * shape[i], shape[j] = shape[j], shape[i] # <<<<<<<<<<<<<< @@ -49428,7 +49104,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { (__pyx_v_shape[__pyx_v_i]) = __pyx_t_6; (__pyx_v_shape[__pyx_v_j]) = __pyx_t_5; - /* "View.MemoryView":952 + /* "View.MemoryView":956 * shape[i], shape[j] = shape[j], shape[i] * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: # <<<<<<<<<<<<<< @@ -49446,16 +49122,16 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_L6_bool_binop_done:; if (__pyx_t_7) { - /* "View.MemoryView":953 + /* "View.MemoryView":957 * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: * _err(ValueError, "Cannot transpose memoryview with indirect dimensions") # <<<<<<<<<<<<<< * * return 1 */ - __pyx_t_9 = __pyx_memoryview_err(__pyx_builtin_ValueError, ((char *)"Cannot transpose memoryview with indirect dimensions")); 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if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 985, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_assign_item_from_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp, __pyx_v_value); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 989, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __pyx_L3:; - /* "View.MemoryView":981 + /* "View.MemoryView":985 * return memoryview.convert_item_to_object(self, itemp) * * cdef assign_item_from_object(self, char *itemp, object value): # <<<<<<<<<<<<<< @@ -49706,7 +49388,7 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo return __pyx_r; } -/* "View.MemoryView":988 +/* "View.MemoryView":992 * * @property * def base(self): # <<<<<<<<<<<<<< @@ -49732,7 +49414,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__", 0); - /* "View.MemoryView":989 + /* "View.MemoryView":993 * @property * def base(self): * return self.from_object # <<<<<<<<<<<<<< @@ -49744,7 +49426,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __pyx_r = __pyx_v_self->from_object; 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@@ -49866,7 +49554,7 @@ static PyObject *__pyx_pf___pyx_memoryviewslice_2__setstate_cython__(CYTHON_UNUS return __pyx_r; } -/* "View.MemoryView":995 +/* "View.MemoryView":999 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -49889,9 +49577,12 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl Py_ssize_t *__pyx_t_7; Py_ssize_t *__pyx_t_8; Py_ssize_t __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_fromslice", 0); - /* "View.MemoryView":1003 + /* "View.MemoryView":1007 * cdef _memoryviewslice result * * if memviewslice.memview == Py_None: # <<<<<<<<<<<<<< @@ -49901,7 +49592,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((((PyObject *)__pyx_v_memviewslice.memview) == Py_None) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1004 + /* "View.MemoryView":1008 * * if memviewslice.memview == Py_None: * return None # <<<<<<<<<<<<<< @@ -49912,7 +49603,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = Py_None; 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- /* "View.MemoryView":1020 + /* "View.MemoryView":1024 * result.view.buf = memviewslice.data * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None # <<<<<<<<<<<<<< @@ -50027,7 +49718,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ ((Py_buffer *)(&__pyx_v_result->__pyx_base.view))->obj = Py_None; - /* "View.MemoryView":1021 + /* "View.MemoryView":1025 * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None * Py_INCREF(Py_None) # <<<<<<<<<<<<<< @@ -50036,7 +49727,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ Py_INCREF(Py_None); - /* "View.MemoryView":1023 + /* "View.MemoryView":1027 * Py_INCREF(Py_None) * * if (memviewslice.memview).flags & PyBUF_WRITABLE: # <<<<<<<<<<<<<< @@ -50046,7 +49737,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((((struct __pyx_memoryview_obj *)__pyx_v_memviewslice.memview)->flags & PyBUF_WRITABLE) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1024 + /* "View.MemoryView":1028 * * if (memviewslice.memview).flags & PyBUF_WRITABLE: * result.flags = PyBUF_RECORDS # <<<<<<<<<<<<<< @@ -50055,7 +49746,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.flags = PyBUF_RECORDS; - /* "View.MemoryView":1023 + /* "View.MemoryView":1027 * Py_INCREF(Py_None) * * if (memviewslice.memview).flags & PyBUF_WRITABLE: # <<<<<<<<<<<<<< @@ -50065,7 +49756,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl goto __pyx_L4; } - /* "View.MemoryView":1026 + /* "View.MemoryView":1030 * result.flags = PyBUF_RECORDS * else: * result.flags = PyBUF_RECORDS_RO # <<<<<<<<<<<<<< @@ -50077,7 +49768,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L4:; - /* "View.MemoryView":1028 + /* "View.MemoryView":1032 * result.flags = PyBUF_RECORDS_RO * * result.view.shape = result.from_slice.shape # <<<<<<<<<<<<<< @@ -50086,7 +49777,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.shape = ((Py_ssize_t *)__pyx_v_result->from_slice.shape); - /* "View.MemoryView":1029 + /* "View.MemoryView":1033 * * result.view.shape = result.from_slice.shape * result.view.strides = result.from_slice.strides # <<<<<<<<<<<<<< @@ -50095,7 +49786,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.strides = ((Py_ssize_t *)__pyx_v_result->from_slice.strides); - /* "View.MemoryView":1032 + /* "View.MemoryView":1036 * * * result.view.suboffsets = NULL # <<<<<<<<<<<<<< @@ -50104,7 +49795,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = NULL; - /* "View.MemoryView":1033 + /* "View.MemoryView":1037 * * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: # <<<<<<<<<<<<<< @@ -50116,7 +49807,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_6 = __pyx_t_8; __pyx_v_suboffset = (__pyx_t_6[0]); - /* "View.MemoryView":1034 + /* "View.MemoryView":1038 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -50126,7 +49817,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1035 + /* "View.MemoryView":1039 * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets # <<<<<<<<<<<<<< @@ -50135,7 +49826,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = ((Py_ssize_t *)__pyx_v_result->from_slice.suboffsets); - /* "View.MemoryView":1036 + /* "View.MemoryView":1040 * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets * break # <<<<<<<<<<<<<< @@ -50144,7 +49835,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ goto __pyx_L6_break; - /* "View.MemoryView":1034 + /* "View.MemoryView":1038 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -50155,7 +49846,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L6_break:; - /* "View.MemoryView":1038 + /* "View.MemoryView":1042 * break * * result.view.len = result.view.itemsize # <<<<<<<<<<<<<< @@ -50165,7 +49856,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_9 = __pyx_v_result->__pyx_base.view.itemsize; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; - /* "View.MemoryView":1039 + /* "View.MemoryView":1043 * * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: # <<<<<<<<<<<<<< @@ -50175,29 +49866,29 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_7 = (__pyx_v_result->__pyx_base.view.shape + __pyx_v_ndim); for (__pyx_t_8 = __pyx_v_result->__pyx_base.view.shape; __pyx_t_8 < __pyx_t_7; __pyx_t_8++) { __pyx_t_6 = __pyx_t_8; - __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1039, __pyx_L1_error) + __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1043, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF_SET(__pyx_v_length, __pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":1040 + /* "View.MemoryView":1044 * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: * result.view.len *= length # <<<<<<<<<<<<<< * * result.to_object_func = to_object_func */ - __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; } - /* "View.MemoryView":1042 + /* "View.MemoryView":1046 * result.view.len *= length * * result.to_object_func = to_object_func # <<<<<<<<<<<<<< @@ -50206,7 +49897,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_object_func = __pyx_v_to_object_func; - /* "View.MemoryView":1043 + /* "View.MemoryView":1047 * * result.to_object_func = to_object_func * result.to_dtype_func = to_dtype_func # <<<<<<<<<<<<<< @@ -50215,7 +49906,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_dtype_func = __pyx_v_to_dtype_func; - /* "View.MemoryView":1045 + /* "View.MemoryView":1049 * result.to_dtype_func = to_dtype_func * * return result # <<<<<<<<<<<<<< @@ -50227,7 +49918,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":995 + /* "View.MemoryView":999 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -50249,11 +49940,11 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl return __pyx_r; } -/* "View.MemoryView":1048 +/* "View.MemoryView":1052 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *mslice): + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj */ @@ -50264,10 +49955,13 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p int __pyx_t_1; int __pyx_t_2; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_slice_from_memview", 0); - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -50277,20 +49971,20 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1052 + /* "View.MemoryView":1056 * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): * obj = memview # <<<<<<<<<<<<<< * return &obj.from_slice * else: */ - if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(2, 1052, __pyx_L1_error) + if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(2, 1056, __pyx_L1_error) __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_obj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":1053 + /* "View.MemoryView":1057 * if isinstance(memview, _memoryviewslice): * obj = memview * return &obj.from_slice # <<<<<<<<<<<<<< @@ -50300,8 +49994,8 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_r = (&__pyx_v_obj->from_slice); goto __pyx_L0; - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -50309,7 +50003,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p */ } - /* "View.MemoryView":1055 + /* "View.MemoryView":1059 * return &obj.from_slice * else: * slice_copy(memview, mslice) # <<<<<<<<<<<<<< @@ -50319,7 +50013,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, __pyx_v_mslice); - /* "View.MemoryView":1056 + /* "View.MemoryView":1060 * else: * slice_copy(memview, mslice) * return mslice # <<<<<<<<<<<<<< @@ -50330,26 +50024,26 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p goto __pyx_L0; } - /* "View.MemoryView":1048 + /* "View.MemoryView":1052 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *mslice): + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj */ /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_WriteUnraisable("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); - __pyx_r = 0; + __Pyx_AddTraceback("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_obj); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "View.MemoryView":1059 +/* "View.MemoryView":1063 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -50370,7 +50064,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem Py_ssize_t __pyx_t_5; __Pyx_RefNannySetupContext("slice_copy", 0); - /* "View.MemoryView":1063 + /* "View.MemoryView":1067 * cdef (Py_ssize_t*) shape, strides, suboffsets * * shape = memview.view.shape # <<<<<<<<<<<<<< @@ -50380,7 +50074,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.shape; __pyx_v_shape = __pyx_t_1; - /* "View.MemoryView":1064 + /* "View.MemoryView":1068 * * shape = memview.view.shape * strides = memview.view.strides # <<<<<<<<<<<<<< @@ -50390,7 +50084,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.strides; __pyx_v_strides = __pyx_t_1; - /* "View.MemoryView":1065 + /* "View.MemoryView":1069 * shape = memview.view.shape * strides = memview.view.strides * suboffsets = memview.view.suboffsets # <<<<<<<<<<<<<< @@ -50400,7 +50094,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.suboffsets; __pyx_v_suboffsets = __pyx_t_1; - /* "View.MemoryView":1067 + /* "View.MemoryView":1071 * suboffsets = memview.view.suboffsets * * dst.memview = <__pyx_memoryview *> memview # <<<<<<<<<<<<<< @@ -50409,7 +50103,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->memview = ((struct __pyx_memoryview_obj *)__pyx_v_memview); - /* "View.MemoryView":1068 + /* "View.MemoryView":1072 * * dst.memview = <__pyx_memoryview *> memview * dst.data = memview.view.buf # <<<<<<<<<<<<<< @@ -50418,7 +50112,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->data = ((char *)__pyx_v_memview->view.buf); - /* "View.MemoryView":1070 + /* "View.MemoryView":1074 * dst.data = memview.view.buf * * for dim in range(memview.view.ndim): # <<<<<<<<<<<<<< @@ -50430,7 +50124,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_dim = __pyx_t_4; - /* "View.MemoryView":1071 + /* "View.MemoryView":1075 * * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] # <<<<<<<<<<<<<< @@ -50439,7 +50133,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->shape[__pyx_v_dim]) = (__pyx_v_shape[__pyx_v_dim]); - /* "View.MemoryView":1072 + /* "View.MemoryView":1076 * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] # <<<<<<<<<<<<<< @@ -50448,7 +50142,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->strides[__pyx_v_dim]) = (__pyx_v_strides[__pyx_v_dim]); - /* "View.MemoryView":1073 + /* "View.MemoryView":1077 * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 # <<<<<<<<<<<<<< @@ -50463,7 +50157,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_5; } - /* "View.MemoryView":1059 + /* "View.MemoryView":1063 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -50475,7 +50169,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1076 +/* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -50488,9 +50182,12 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; 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if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1084, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "View.MemoryView":1076 + /* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -50532,7 +50229,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx return __pyx_r; } -/* "View.MemoryView":1083 +/* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -50550,9 +50247,12 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview PyObject *(*__pyx_t_3)(char *); int (*__pyx_t_4)(char *, PyObject *); PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy_from_slice", 0); - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -50563,7 +50263,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1091 + /* "View.MemoryView":1095 * * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func # <<<<<<<<<<<<<< @@ -50573,7 +50273,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; __pyx_v_to_object_func = __pyx_t_3; - /* "View.MemoryView":1092 + /* "View.MemoryView":1096 * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< @@ -50583,7 +50283,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; __pyx_v_to_dtype_func = __pyx_t_4; - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -50593,7 +50293,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview goto __pyx_L3; } - /* "View.MemoryView":1094 + /* "View.MemoryView":1098 * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func * else: * to_object_func = NULL # <<<<<<<<<<<<<< @@ -50603,7 +50303,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview /*else*/ { __pyx_v_to_object_func = NULL; - /* "View.MemoryView":1095 + /* "View.MemoryView":1099 * else: * to_object_func = NULL * to_dtype_func = NULL # <<<<<<<<<<<<<< @@ -50614,7 +50314,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview } __pyx_L3:; - /* "View.MemoryView":1097 + /* "View.MemoryView":1101 * to_dtype_func = NULL * * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< @@ -50623,20 +50323,20 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __Pyx_XDECREF(__pyx_r); - /* "View.MemoryView":1099 + /* "View.MemoryView":1103 * return memoryview_fromslice(memviewslice[0], memview.view.ndim, * to_object_func, to_dtype_func, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 1097, __pyx_L1_error) + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 1101, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":1083 + /* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -50655,7 +50355,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview return __pyx_r; } -/* "View.MemoryView":1105 +/* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -50667,7 +50367,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { Py_ssize_t __pyx_r; int __pyx_t_1; - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -50677,7 +50377,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_t_1 = ((__pyx_v_arg < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1107 + /* "View.MemoryView":1111 * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: * return -arg # <<<<<<<<<<<<<< @@ -50687,7 +50387,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_r = (-__pyx_v_arg); goto __pyx_L0; - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -50696,7 +50396,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { */ } - /* "View.MemoryView":1109 + /* "View.MemoryView":1113 * return -arg * else: * return arg # <<<<<<<<<<<<<< @@ -50708,7 +50408,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { goto __pyx_L0; } - /* "View.MemoryView":1105 + /* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -50721,7 +50421,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { return __pyx_r; } -/* "View.MemoryView":1112 +/* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -50739,7 +50439,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ int __pyx_t_3; int __pyx_t_4; - /* "View.MemoryView":1117 + /* "View.MemoryView":1121 * """ * cdef int i * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< @@ -50748,7 +50448,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = 0; - /* "View.MemoryView":1118 + /* "View.MemoryView":1122 * cdef int i * cdef Py_ssize_t c_stride = 0 * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< @@ -50757,7 +50457,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = 0; - /* "View.MemoryView":1120 + /* "View.MemoryView":1124 * cdef Py_ssize_t f_stride = 0 * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -50767,7 +50467,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -50777,7 +50477,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1122 + /* "View.MemoryView":1126 * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -50786,7 +50486,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1123 + /* "View.MemoryView":1127 * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -50795,7 +50495,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L4_break; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -50806,7 +50506,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L4_break:; - /* "View.MemoryView":1125 + /* "View.MemoryView":1129 * break * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -50818,7 +50518,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -50828,7 +50528,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1127 + /* "View.MemoryView":1131 * for i in range(ndim): * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -50837,7 +50537,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1128 + /* "View.MemoryView":1132 * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -50846,7 +50546,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L7_break; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -50857,7 +50557,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L7_break:; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -50867,7 +50567,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1131 + /* "View.MemoryView":1135 * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): * return 'C' # <<<<<<<<<<<<<< @@ -50877,7 +50577,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_r = 'C'; goto __pyx_L0; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -50886,7 +50586,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ } - /* "View.MemoryView":1133 + /* "View.MemoryView":1137 * return 'C' * else: * return 'F' # <<<<<<<<<<<<<< @@ -50898,7 +50598,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ goto __pyx_L0; } - /* "View.MemoryView":1112 + /* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -50911,7 +50611,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ return __pyx_r; } -/* "View.MemoryView":1136 +/* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -50932,7 +50632,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v Py_ssize_t __pyx_t_5; Py_ssize_t __pyx_t_6; - /* "View.MemoryView":1143 + /* "View.MemoryView":1147 * * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< @@ -50941,7 +50641,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_extent = (__pyx_v_src_shape[0]); - /* "View.MemoryView":1144 + /* "View.MemoryView":1148 * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< @@ -50950,7 +50650,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - /* "View.MemoryView":1145 + /* "View.MemoryView":1149 * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< @@ -50959,7 +50659,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_stride = (__pyx_v_src_strides[0]); - /* "View.MemoryView":1146 + /* "View.MemoryView":1150 * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< @@ -50968,7 +50668,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -50978,7 +50678,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -50998,7 +50698,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L5_bool_binop_done; } - /* "View.MemoryView":1150 + /* "View.MemoryView":1154 * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< @@ -51013,7 +50713,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = __pyx_t_3; __pyx_L5_bool_binop_done:; - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -51022,7 +50722,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ if (__pyx_t_1) { - /* "View.MemoryView":1151 + /* "View.MemoryView":1155 * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< @@ -51031,7 +50731,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -51041,7 +50741,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L4; } - /* "View.MemoryView":1153 + /* "View.MemoryView":1157 * memcpy(dst_data, src_data, itemsize * dst_extent) * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -51054,7 +50754,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1154 + /* "View.MemoryView":1158 * else: * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< @@ -51063,7 +50763,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - /* "View.MemoryView":1155 + /* "View.MemoryView":1159 * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -51072,7 +50772,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1156 + /* "View.MemoryView":1160 * memcpy(dst_data, src_data, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -51084,7 +50784,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L4:; - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -51094,7 +50794,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L3; } - /* "View.MemoryView":1158 + /* "View.MemoryView":1162 * dst_data += dst_stride * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -51107,7 +50807,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1159 + /* "View.MemoryView":1163 * else: * for i in range(dst_extent): * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< @@ -51116,7 +50816,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - /* "View.MemoryView":1163 + /* "View.MemoryView":1167 * src_shape + 1, dst_shape + 1, * ndim - 1, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -51125,7 +50825,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1164 + /* "View.MemoryView":1168 * ndim - 1, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -51137,7 +50837,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L3:; - /* "View.MemoryView":1136 + /* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -51148,7 +50848,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v /* function exit code */ } -/* "View.MemoryView":1166 +/* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -51158,7 +50858,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - /* "View.MemoryView":1169 + /* "View.MemoryView":1173 * __Pyx_memviewslice *dst, * int ndim, size_t itemsize) nogil: * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< @@ -51167,7 +50867,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi */ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1166 + /* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -51178,57 +50878,57 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi /* function exit code */ } -/* "View.MemoryView":1173 +/* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - int __pyx_v_i; + Py_ssize_t __pyx_v_shape; Py_ssize_t __pyx_v_size; Py_ssize_t __pyx_r; Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; + Py_ssize_t *__pyx_t_2; + Py_ssize_t *__pyx_t_3; + Py_ssize_t *__pyx_t_4; - /* "View.MemoryView":1176 + /* "View.MemoryView":1179 + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< * - * for i in range(ndim): + * for shape in src.shape[:ndim]: */ __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_size = __pyx_t_1; - /* "View.MemoryView":1178 - * cdef Py_ssize_t size = src.memview.view.itemsize + /* "View.MemoryView":1181 + * cdef Py_ssize_t shape, size = src.memview.view.itemsize * - * for i in range(ndim): # <<<<<<<<<<<<<< - * size *= src.shape[i] + * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< + * size *= shape * */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; + __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); + for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { + __pyx_t_2 = __pyx_t_4; + __pyx_v_shape = (__pyx_t_2[0]); - /* "View.MemoryView":1179 + /* "View.MemoryView":1182 * - * for i in range(ndim): - * size *= src.shape[i] # <<<<<<<<<<<<<< + * for shape in src.shape[:ndim]: + * size *= shape # <<<<<<<<<<<<<< * * return size */ - __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + __pyx_v_size = (__pyx_v_size * __pyx_v_shape); } - /* "View.MemoryView":1181 - * size *= src.shape[i] + /* "View.MemoryView":1184 + * size *= shape * * return size # <<<<<<<<<<<<<< * @@ -51237,12 +50937,12 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_r = __pyx_v_size; goto __pyx_L0; - /* "View.MemoryView":1173 + /* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ /* function exit code */ @@ -51250,7 +50950,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr return __pyx_r; } -/* "View.MemoryView":1184 +/* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -51266,7 +50966,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ int __pyx_t_3; int __pyx_t_4; - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -51276,38 +50976,38 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_t_1 = ((__pyx_v_order == 'F') != 0); if (__pyx_t_1) { - /* "View.MemoryView":1194 + /* "View.MemoryView":1197 * * if order == 'F': * for idx in range(ndim): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ __pyx_t_2 = __pyx_v_ndim; __pyx_t_3 = __pyx_t_2; for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_idx = __pyx_t_4; - /* "View.MemoryView":1195 + /* "View.MemoryView":1198 * if order == 'F': * for idx in range(ndim): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * else: */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1196 + /* "View.MemoryView":1199 * for idx in range(ndim): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * else: * for idx in range(ndim - 1, -1, -1): */ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); } - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -51317,30 +51017,30 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ goto __pyx_L3; } - /* "View.MemoryView":1198 - * stride = stride * shape[idx] + /* "View.MemoryView":1201 + * stride *= shape[idx] * else: * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ /*else*/ { for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; - /* "View.MemoryView":1199 + /* "View.MemoryView":1202 * else: * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1200 + /* "View.MemoryView":1203 * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * * return stride */ @@ -51349,8 +51049,8 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ } __pyx_L3:; - /* "View.MemoryView":1202 - * stride = stride * shape[idx] + /* "View.MemoryView":1205 + * stride *= shape[idx] * * return stride # <<<<<<<<<<<<<< * @@ -51359,7 +51059,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_r = __pyx_v_stride; goto __pyx_L0; - /* "View.MemoryView":1184 + /* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -51372,7 +51072,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ return __pyx_r; } -/* "View.MemoryView":1205 +/* "View.MemoryView":1208 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -51392,8 +51092,11 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, struct __pyx_memoryview_obj *__pyx_t_4; int __pyx_t_5; int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; - /* "View.MemoryView":1216 + /* "View.MemoryView":1219 * cdef void *result * * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -51403,7 +51106,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1217 + /* "View.MemoryView":1220 * * cdef size_t itemsize = src.memview.view.itemsize * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< @@ -51412,7 +51115,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - /* "View.MemoryView":1219 + /* "View.MemoryView":1222 * cdef size_t size = slice_get_size(src, ndim) * * result = malloc(size) # <<<<<<<<<<<<<< @@ -51421,7 +51124,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_result = malloc(__pyx_v_size); - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -51431,16 +51134,16 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1221 + /* "View.MemoryView":1224 * result = malloc(size) * if not result: * _err(MemoryError, NULL) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1221, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1224, __pyx_L1_error) - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -51449,7 +51152,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ } - /* "View.MemoryView":1224 + /* "View.MemoryView":1227 * * * tmpslice.data = result # <<<<<<<<<<<<<< @@ -51458,7 +51161,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - /* "View.MemoryView":1225 + /* "View.MemoryView":1228 * * tmpslice.data = result * tmpslice.memview = src.memview # <<<<<<<<<<<<<< @@ -51468,7 +51171,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_4 = __pyx_v_src->memview; __pyx_v_tmpslice->memview = __pyx_t_4; - /* "View.MemoryView":1226 + /* "View.MemoryView":1229 * tmpslice.data = result * tmpslice.memview = src.memview * for i in range(ndim): # <<<<<<<<<<<<<< @@ -51480,7 +51183,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1227 + /* "View.MemoryView":1230 * tmpslice.memview = src.memview * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< @@ -51489,7 +51192,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - /* "View.MemoryView":1228 + /* "View.MemoryView":1231 * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -51499,7 +51202,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1230 + /* "View.MemoryView":1233 * tmpslice.suboffsets[i] = -1 * * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< @@ -51508,7 +51211,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - /* "View.MemoryView":1234 + /* "View.MemoryView":1237 * * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -51520,7 +51223,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1235 + /* "View.MemoryView":1238 * * for i in range(ndim): * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< @@ -51530,7 +51233,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1236 + /* "View.MemoryView":1239 * for i in range(ndim): * if tmpslice.shape[i] == 1: * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< @@ -51539,7 +51242,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (__pyx_v_tmpslice->strides[__pyx_v_i]) = 0; - /* "View.MemoryView":1235 + /* "View.MemoryView":1238 * * for i in range(ndim): * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< @@ -51549,7 +51252,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, } } - /* "View.MemoryView":1238 + /* "View.MemoryView":1241 * tmpslice.strides[i] = 0 * * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< @@ -51559,7 +51262,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = (__pyx_memviewslice_is_contig((__pyx_v_src[0]), __pyx_v_order, __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1239 + /* "View.MemoryView":1242 * * if slice_is_contig(src[0], order, ndim): * memcpy(result, src.data, size) # <<<<<<<<<<<<<< @@ -51568,7 +51271,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size)); - /* "View.MemoryView":1238 + /* "View.MemoryView":1241 * tmpslice.strides[i] = 0 * * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< @@ -51578,7 +51281,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, goto __pyx_L9; } - /* "View.MemoryView":1241 + /* "View.MemoryView":1244 * memcpy(result, src.data, size) * else: * copy_strided_to_strided(src, tmpslice, ndim, itemsize) # <<<<<<<<<<<<<< @@ -51590,7 +51293,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, } __pyx_L9:; - /* "View.MemoryView":1243 + /* "View.MemoryView":1246 * copy_strided_to_strided(src, tmpslice, ndim, itemsize) * * return result # <<<<<<<<<<<<<< @@ -51600,7 +51303,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "View.MemoryView":1205 + /* "View.MemoryView":1208 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -51624,7 +51327,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, return __pyx_r; 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- /* "View.MemoryView":1286 + /* "View.MemoryView":1289 * broadcast_leading(&dst, dst_ndim, src_ndim) * * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -52044,7 +51759,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_v_ndim = __pyx_t_5; - /* "View.MemoryView":1288 + /* "View.MemoryView":1291 * cdef int ndim = max(src_ndim, dst_ndim) * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -52056,7 +51771,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -52066,7 +51781,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -52076,7 +51791,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1291 + /* "View.MemoryView":1294 * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: * broadcasting = True # <<<<<<<<<<<<<< @@ -52085,7 +51800,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 1; - /* "View.MemoryView":1292 + /* "View.MemoryView":1295 * if src.shape[i] == 1: * broadcasting = True * src.strides[i] = 0 # <<<<<<<<<<<<<< @@ -52094,7 +51809,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (__pyx_v_src.strides[__pyx_v_i]) = 0; - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -52104,7 +51819,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L7; } - /* "View.MemoryView":1294 + /* "View.MemoryView":1297 * src.strides[i] = 0 * else: * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< @@ -52112,11 +51827,11 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if src.suboffsets[i] >= 0: */ /*else*/ { - __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1294, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1297, __pyx_L1_error) } __pyx_L7:; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -52125,7 +51840,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -52135,16 +51850,16 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1297 + /* "View.MemoryView":1300 * * if src.suboffsets[i] >= 0: * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< * * if slices_overlap(&src, &dst, ndim, itemsize): */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1297, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1300, __pyx_L1_error) - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -52154,7 +51869,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } } - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -52164,7 +51879,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -52174,7 +51889,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1302 + /* "View.MemoryView":1305 * * if not slice_is_contig(src, order, ndim): * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< @@ -52183,7 +51898,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -52192,17 +51907,17 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1304 + /* "View.MemoryView":1307 * order = get_best_order(&dst, ndim) * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< * src = tmp * */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1304, __pyx_L1_error) + __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1307, __pyx_L1_error) __pyx_v_tmpdata = __pyx_t_7; - /* "View.MemoryView":1305 + /* "View.MemoryView":1308 * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) * src = tmp # <<<<<<<<<<<<<< @@ -52211,7 +51926,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_src = __pyx_v_tmp; - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -52220,7 +51935,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -52230,7 +51945,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -52240,7 +51955,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1311 + /* "View.MemoryView":1314 * * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< @@ -52249,7 +51964,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -52259,7 +51974,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L12; } - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -52269,7 +51984,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1313 + /* "View.MemoryView":1316 * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< @@ -52278,7 +51993,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -52288,7 +52003,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_L12:; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -52298,7 +52013,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_v_direct_copy != 0); if (__pyx_t_2) { - /* "View.MemoryView":1317 + /* "View.MemoryView":1320 * if direct_copy: * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -52307,7 +52022,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1318 + /* "View.MemoryView":1321 * * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< @@ -52316,7 +52031,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - /* "View.MemoryView":1319 + /* "View.MemoryView":1322 * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -52325,7 +52040,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1320 + /* "View.MemoryView":1323 * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) # <<<<<<<<<<<<<< @@ -52334,7 +52049,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1321 + /* "View.MemoryView":1324 * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -52344,7 +52059,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -52353,7 +52068,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -52362,7 +52077,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -52376,25 +52091,25 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_8 = (__pyx_t_2 != 0); if (__pyx_t_8) { - /* "View.MemoryView":1326 + /* "View.MemoryView":1329 * * * transpose_memslice(&src) # <<<<<<<<<<<<<< * transpose_memslice(&dst) * */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1326, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1329, __pyx_L1_error) - /* "View.MemoryView":1327 + /* "View.MemoryView":1330 * * transpose_memslice(&src) * transpose_memslice(&dst) # <<<<<<<<<<<<<< * * refcount_copying(&dst, dtype_is_object, ndim, False) */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1327, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1330, __pyx_L1_error) - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -52403,7 +52118,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1329 + /* "View.MemoryView":1332 * transpose_memslice(&dst) * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -52412,7 +52127,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1330 + /* "View.MemoryView":1333 * * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< @@ -52421,7 +52136,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1331 + /* "View.MemoryView":1334 * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -52430,7 +52145,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1333 + /* "View.MemoryView":1336 * refcount_copying(&dst, dtype_is_object, ndim, True) * * free(tmpdata) # <<<<<<<<<<<<<< @@ -52439,7 +52154,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1334 + /* "View.MemoryView":1337 * * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -52449,7 +52164,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1265 + /* "View.MemoryView":1268 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -52473,7 +52188,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ return __pyx_r; } -/* "View.MemoryView":1337 +/* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -52488,7 +52203,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1341 + /* "View.MemoryView":1344 * int ndim_other) nogil: * cdef int i * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< @@ -52497,7 +52212,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); - /* "View.MemoryView":1343 + /* "View.MemoryView":1346 * cdef int offset = ndim_other - ndim * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -52507,7 +52222,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1344 + /* "View.MemoryView":1347 * * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< @@ -52516,7 +52231,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); - /* "View.MemoryView":1345 + /* "View.MemoryView":1348 * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< @@ -52525,7 +52240,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1346 + /* "View.MemoryView":1349 * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< @@ -52535,7 +52250,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); } - /* "View.MemoryView":1348 + /* "View.MemoryView":1351 * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * * for i in range(offset): # <<<<<<<<<<<<<< @@ -52547,7 +52262,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1349 + /* "View.MemoryView":1352 * * for i in range(offset): * mslice.shape[i] = 1 # <<<<<<<<<<<<<< @@ -52556,7 +52271,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[__pyx_v_i]) = 1; - /* "View.MemoryView":1350 + /* "View.MemoryView":1353 * for i in range(offset): * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< @@ -52565,7 +52280,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); - /* "View.MemoryView":1351 + /* "View.MemoryView":1354 * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] * mslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -52575,7 +52290,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1337 + /* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -52586,7 +52301,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic /* function exit code */ } -/* "View.MemoryView":1359 +/* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -52597,7 +52312,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { int __pyx_t_1; - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -52607,7 +52322,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __pyx_t_1 = (__pyx_v_dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":1364 + /* "View.MemoryView":1367 * * if dtype_is_object: * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< @@ -52616,7 +52331,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -52625,7 +52340,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ } - /* "View.MemoryView":1359 + /* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -52636,7 +52351,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i /* function exit code */ } -/* "View.MemoryView":1368 +/* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52651,7 +52366,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0); - /* "View.MemoryView":1371 + /* "View.MemoryView":1374 * Py_ssize_t *strides, int ndim, * bint inc) with gil: * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<< @@ -52660,7 +52375,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1368 + /* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52675,7 +52390,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif } -/* "View.MemoryView":1374 +/* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52692,7 +52407,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss int __pyx_t_4; __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); - /* "View.MemoryView":1378 + /* "View.MemoryView":1381 * cdef Py_ssize_t i * * for i in range(shape[0]): # <<<<<<<<<<<<<< @@ -52704,7 +52419,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -52714,7 +52429,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_4) { - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -52724,7 +52439,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = (__pyx_v_inc != 0); if (__pyx_t_4) { - /* "View.MemoryView":1381 + /* "View.MemoryView":1384 * if ndim == 1: * if inc: * Py_INCREF(( data)[0]) # <<<<<<<<<<<<<< @@ -52733,7 +52448,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ Py_INCREF((((PyObject **)__pyx_v_data)[0])); - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -52743,7 +52458,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L6; } - /* "View.MemoryView":1383 + /* "View.MemoryView":1386 * Py_INCREF(( data)[0]) * else: * Py_DECREF(( data)[0]) # <<<<<<<<<<<<<< @@ -52755,7 +52470,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L6:; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -52765,7 +52480,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L5; } - /* "View.MemoryView":1385 + /* "View.MemoryView":1388 * Py_DECREF(( data)[0]) * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -52774,7 +52489,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ /*else*/ { - /* "View.MemoryView":1386 + /* "View.MemoryView":1389 * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, * ndim - 1, inc) # <<<<<<<<<<<<<< @@ -52785,7 +52500,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L5:; - /* "View.MemoryView":1388 + /* "View.MemoryView":1391 * ndim - 1, inc) * * data += strides[0] # <<<<<<<<<<<<<< @@ -52795,7 +52510,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_v_data = (__pyx_v_data + (__pyx_v_strides[0])); } - /* "View.MemoryView":1374 + /* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52807,7 +52522,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1394 +/* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -52817,7 +52532,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item, int __pyx_v_dtype_is_object) { - /* "View.MemoryView":1397 + /* "View.MemoryView":1400 * size_t itemsize, void *item, * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -52826,7 +52541,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1398 + /* "View.MemoryView":1401 * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< @@ -52835,7 +52550,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1400 + /* "View.MemoryView":1403 * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, * itemsize, item) * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -52844,7 +52559,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1394 + /* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -52855,7 +52570,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst /* function exit code */ } -/* "View.MemoryView":1404 +/* "View.MemoryView":1407 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52872,7 +52587,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t Py_ssize_t __pyx_t_3; Py_ssize_t __pyx_t_4; - /* "View.MemoryView":1408 + /* "View.MemoryView":1411 * size_t itemsize, void *item) nogil: * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] # <<<<<<<<<<<<<< @@ -52881,7 +52596,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_stride = (__pyx_v_strides[0]); - /* "View.MemoryView":1409 + /* "View.MemoryView":1412 * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] * cdef Py_ssize_t extent = shape[0] # <<<<<<<<<<<<<< @@ -52890,7 +52605,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_extent = (__pyx_v_shape[0]); - /* "View.MemoryView":1411 + /* "View.MemoryView":1414 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -52900,7 +52615,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1412 + /* "View.MemoryView":1415 * * if ndim == 1: * for i in range(extent): # <<<<<<<<<<<<<< @@ -52912,7 +52627,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1413 + /* "View.MemoryView":1416 * if ndim == 1: * for i in range(extent): * memcpy(data, item, itemsize) # <<<<<<<<<<<<<< @@ -52921,7 +52636,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize)); - /* "View.MemoryView":1414 + /* "View.MemoryView":1417 * for i in range(extent): * memcpy(data, item, itemsize) * data += stride # <<<<<<<<<<<<<< @@ -52931,7 +52646,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_v_data = (__pyx_v_data + __pyx_v_stride); } - /* "View.MemoryView":1411 + /* "View.MemoryView":1414 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -52941,7 +52656,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t goto __pyx_L3; } - /* "View.MemoryView":1416 + /* "View.MemoryView":1419 * data += stride * else: * for i in range(extent): # <<<<<<<<<<<<<< @@ -52954,7 +52669,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1417 + /* "View.MemoryView":1420 * else: * for i in range(extent): * _slice_assign_scalar(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -52963,7 +52678,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_memoryview__slice_assign_scalar(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1419 + /* "View.MemoryView":1422 * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) * data += stride # <<<<<<<<<<<<<< @@ -52975,7 +52690,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t } __pyx_L3:; - /* "View.MemoryView":1404 + /* "View.MemoryView":1407 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -52999,6 +52714,9 @@ static PyObject *__pyx_pw_15View_dot_MemoryView_1__pyx_unpickle_Enum(PyObject *_ PyObject *__pyx_v___pyx_type = 0; long __pyx_v___pyx_checksum; PyObject *__pyx_v___pyx_state = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_unpickle_Enum (wrapper)", 0); @@ -53076,6 +52794,9 @@ static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSE PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_unpickle_Enum", 0); /* "(tree fragment)":4 @@ -53264,6 +52985,9 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ PyObject *__pyx_t_6 = NULL; PyObject *__pyx_t_7 = NULL; PyObject *__pyx_t_8 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_unpickle_Enum__set_state", 0); /* "(tree fragment)":12 @@ -53405,9 +53129,9 @@ static void __pyx_tp_dealloc_array(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_array___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->mode); @@ -53500,7 +53224,12 @@ static PyTypeObject __pyx_type___pyx_array = { sizeof(struct __pyx_array_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_array, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -53553,6 +53282,9 @@ static PyTypeObject __pyx_type___pyx_array = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { @@ -53611,7 +53343,12 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_Enum, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -53664,6 +53401,9 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; @@ -53700,9 +53440,9 @@ static void __pyx_tp_dealloc_memoryview(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_memoryview___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->obj); @@ -53864,7 +53604,12 @@ static PyTypeObject __pyx_type___pyx_memoryview = { sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 @@ -53917,6 +53662,9 @@ static PyTypeObject __pyx_type___pyx_memoryview = { #if PY_VERSION_HEX >= 0x030800b1 0, /*tp_vectorcall*/ #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif }; 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- __Pyx_GIVEREF(__pyx_tuple__15); + __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__13)) __PYX_ERR(2, 136, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__13); + __Pyx_GIVEREF(__pyx_tuple__13); /* "View.MemoryView":148 * @@ -54411,9 +54143,9 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(2, 148, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__16); - __Pyx_GIVEREF(__pyx_tuple__16); + __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__14)) __PYX_ERR(2, 148, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__14); + __Pyx_GIVEREF(__pyx_tuple__14); /* "View.MemoryView":176 * self.data = malloc(self.len) @@ -54422,9 +54154,9 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { * * if self.dtype_is_object: */ - __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); 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if (unlikely(!__pyx_t_20)) __PYX_ERR(2, 995, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_20); - if (PyDict_SetItem((PyObject *)__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_20) < 0) __PYX_ERR(2, 991, __pyx_L1_error) + if (PyDict_SetItem((PyObject *)__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_20) < 0) __PYX_ERR(2, 995, __pyx_L1_error) __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; PyType_Modified(__pyx_memoryviewslice_type); @@ -56220,7 +55963,7 @@ static int __Pyx_ParseOptionalKeywords( } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + if (likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { @@ -56247,7 +55990,7 @@ static int __Pyx_ParseOptionalKeywords( while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -56263,7 +56006,7 @@ static int __Pyx_ParseOptionalKeywords( while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -56378,7 +56121,7 @@ static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args return result; } #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); PyObject *globals = PyFunction_GET_GLOBALS(func); PyObject *argdefs = PyFunction_GET_DEFAULTS(func); @@ -56449,12 +56192,12 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, } #if PY_MAJOR_VERSION >= 3 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, kwdefs, closure); #else result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, closure); #endif @@ -57401,7 +57144,7 @@ __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, int i, retval=-1; Py_buffer *buf = &memview->view; __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (memviewslice->memview || memviewslice->data) { + if (unlikely(memviewslice->memview || memviewslice->data)) { PyErr_SetString(PyExc_ValueError, "memviewslice is already initialized!"); goto fail; @@ -57480,13 +57223,13 @@ __Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int first_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview || (PyObject *) memview == Py_None) + if (unlikely(!memview || (PyObject *) memview == Py_None)) return; - if (__pyx_get_slice_count(memview) < 0) + if (unlikely(__pyx_get_slice_count(memview) < 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); first_time = __pyx_add_acquisition_count(memview) == 0; - if (first_time) { + if (unlikely(first_time)) { if (have_gil) { Py_INCREF((PyObject *) memview); } else { @@ -57500,18 +57243,16 @@ static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int last_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview ) { - return; - } else if ((PyObject *) memview == Py_None) { + if (unlikely(!memview || (PyObject *) memview == Py_None)) { memslice->memview = NULL; return; } - if (__pyx_get_slice_count(memview) <= 0) + if (unlikely(__pyx_get_slice_count(memview) <= 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); last_time = __pyx_sub_acquisition_count(memview) == 1; memslice->data = NULL; - if (last_time) { + if (unlikely(last_time)) { if (have_gil) { Py_CLEAR(memslice->memview); } else { @@ -58058,9 +57799,9 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( if (stop < 0) stop += length; } - length = stop - start; - if (unlikely(length <= 0)) + if (unlikely(stop <= start)) return PyUnicode_FromUnicode(NULL, 0); + length = stop - start; cstring += start; if (decode_func) { return decode_func(cstring, length, errors); @@ -58149,7 +57890,7 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { { #if PY_MAJOR_VERSION >= 3 if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { + if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); if (!module) { @@ -58297,48 +58038,6 @@ static CYTHON_INLINE long __Pyx_div_long(long a, long b) { return q; } -/* WriteUnraisableException */ -static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, - CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback, CYTHON_UNUSED int nogil) { - PyObject *old_exc, *old_val, *old_tb; - PyObject *ctx; - __Pyx_PyThreadState_declare -#ifdef WITH_THREAD - PyGILState_STATE state; - if (nogil) - state = PyGILState_Ensure(); -#ifdef _MSC_VER - else state = (PyGILState_STATE)-1; -#endif -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); - if (full_traceback) { - Py_XINCREF(old_exc); - Py_XINCREF(old_val); - Py_XINCREF(old_tb); - __Pyx_ErrRestore(old_exc, old_val, old_tb); - PyErr_PrintEx(1); - } - #if PY_MAJOR_VERSION < 3 - ctx = PyString_FromString(name); - #else - ctx = PyUnicode_FromString(name); - #endif - __Pyx_ErrRestore(old_exc, old_val, old_tb); - if (!ctx) { - PyErr_WriteUnraisable(Py_None); - } else { - PyErr_WriteUnraisable(ctx); - Py_DECREF(ctx); - } -#ifdef WITH_THREAD - if (nogil) - PyGILState_Release(state); -#endif -} - /* ImportFrom */ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); @@ -58439,6 +58138,28 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable) { return -1; } +/* PyObjectGetAttrStrNoError */ +static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + __Pyx_PyErr_Clear(); +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { + return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); + } +#endif + result = __Pyx_PyObject_GetAttrStr(obj, attr_name); + if (unlikely(!result)) { + __Pyx_PyObject_GetAttrStr_ClearAttributeError(); + } + return result; +} + /* SetupReduce */ static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { int ret; @@ -58466,43 +58187,51 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { PyObject *setstate = NULL; PyObject *setstate_cython = NULL; #if CYTHON_USE_PYTYPE_LOOKUP - if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #else - if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #endif #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; if (reduce_ex == object_reduce_ex) { #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); + if (likely(reduce_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (reduce == object_reduce || PyErr_Occurred()) { + goto __PYX_BAD; + } setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); if (!setstate) PyErr_Clear(); if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); + if (likely(setstate_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (!setstate || PyErr_Occurred()) { + goto __PYX_BAD; + } } PyType_Modified((PyTypeObject*)type_obj); } } - goto GOOD; -BAD: + goto __PYX_GOOD; +__PYX_BAD: if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); ret = -1; -GOOD: +__PYX_GOOD: #if !CYTHON_USE_PYTYPE_LOOKUP Py_XDECREF(object_reduce); Py_XDECREF(object_reduce_ex); @@ -58615,7 +58344,7 @@ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { goto done; } -/* CythonFunction */ +/* CythonFunctionShared */ #include static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) @@ -58922,10 +58651,9 @@ static PyMethodDef __pyx_CyFunction_methods[] = { #else #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func.m_weakreflist) #endif -static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, - PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { - __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); - if (op == NULL) +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { + if (unlikely(op == NULL)) return NULL; op->flags = flags; __Pyx_CyFunction_weakreflist(op) = NULL; @@ -58946,12 +58674,12 @@ static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int f Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; + op->defaults_size = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_kwdict = NULL; op->defaults_getter = NULL; op->func_annotations = NULL; - PyObject_GC_Track(op); return (PyObject *) op; } static int @@ -59181,6 +58909,9 @@ static PyTypeObject __pyx_CyFunctionType_type = { #if PY_VERSION_HEX >= 0x030800b1 0, #endif +#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, +#endif }; static int __pyx_CyFunction_init(void) { __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); @@ -59196,6 +58927,7 @@ static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t return PyErr_NoMemory(); memset(m->defaults, 0, size); m->defaults_pyobjects = pyobjects; + m->defaults_size = size; return m->defaults; } static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { @@ -59216,20 +58948,23 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py /* FusedFunction */ static PyObject * -__pyx_FusedFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, - PyObject *qualname, PyObject *self, +__pyx_FusedFunction_New(PyMethodDef *ml, int flags, + PyObject *qualname, PyObject *closure, PyObject *module, PyObject *globals, PyObject *code) { - __pyx_FusedFunctionObject *fusedfunc = - (__pyx_FusedFunctionObject *) __Pyx_CyFunction_New(type, ml, flags, qualname, - self, module, globals, code); - if (!fusedfunc) - return NULL; - fusedfunc->__signatures__ = NULL; - fusedfunc->type = NULL; - fusedfunc->self = NULL; - return (PyObject *) fusedfunc; + PyObject *op = __Pyx_CyFunction_Init( + PyObject_GC_New(__pyx_CyFunctionObject, __pyx_FusedFunctionType), + ml, flags, qualname, closure, module, globals, code + ); + if (likely(op)) { + __pyx_FusedFunctionObject *fusedfunc = (__pyx_FusedFunctionObject *) op; + fusedfunc->__signatures__ = NULL; + fusedfunc->type = NULL; + fusedfunc->self = NULL; + PyObject_GC_Track(op); + } + return op; } static void __pyx_FusedFunction_dealloc(__pyx_FusedFunctionObject *self) @@ -59269,7 +59004,7 @@ __pyx_FusedFunction_descr_get(PyObject *self, PyObject *obj, PyObject *type) } if (obj == Py_None) obj = NULL; - meth = (__pyx_FusedFunctionObject *) __pyx_FusedFunction_NewEx( + meth = (__pyx_FusedFunctionObject *) __pyx_FusedFunction_New( ((PyCFunctionObject *) func)->m_ml, ((__pyx_CyFunctionObject *) func)->flags, ((__pyx_CyFunctionObject *) func)->func_qualname, @@ -59279,6 +59014,20 @@ __pyx_FusedFunction_descr_get(PyObject *self, PyObject *obj, PyObject *type) ((__pyx_CyFunctionObject *) func)->func_code); if (!meth) return NULL; + if (func->func.defaults) { + PyObject **pydefaults; + int i; + if (!__Pyx_CyFunction_InitDefaults((PyObject*)meth, + func->func.defaults_size, + func->func.defaults_pyobjects)) { + Py_XDECREF((PyObject*)meth); + return NULL; + } + memcpy(meth->func.defaults, func->func.defaults, func->func.defaults_size); + pydefaults = __Pyx_CyFunction_Defaults(PyObject *, meth); + for (i = 0; i < meth->func.defaults_pyobjects; i++) + Py_XINCREF(pydefaults[i]); + } Py_XINCREF(func->func.func_classobj); meth->func.func_classobj = func->func.func_classobj; Py_XINCREF(func->__signatures__); @@ -59314,27 +59063,29 @@ __pyx_FusedFunction_getitem(__pyx_FusedFunctionObject *self, PyObject *idx) if (PyTuple_Check(idx)) { PyObject *list = PyList_New(0); Py_ssize_t n = PyTuple_GET_SIZE(idx); - PyObject *string = NULL; PyObject *sep = NULL; int i; - if (!list) + if (unlikely(!list)) return NULL; for (i = 0; i < n; i++) { + int ret; + PyObject *string; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS PyObject *item = PyTuple_GET_ITEM(idx, i); #else - PyObject *item = PySequence_ITEM(idx, i); + PyObject *item = PySequence_ITEM(idx, i); if (unlikely(!item)) goto __pyx_err; #endif string = _obj_to_str(item); #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) Py_DECREF(item); #endif - if (!string || PyList_Append(list, string) < 0) - goto __pyx_err; + if (unlikely(!string)) goto __pyx_err; + ret = PyList_Append(list, string); Py_DECREF(string); + if (unlikely(ret < 0)) goto __pyx_err; } sep = PyUnicode_FromString("|"); - if (sep) + if (likely(sep)) signature = PyUnicode_Join(sep, list); __pyx_err: ; @@ -59538,8 +59289,12 @@ static PyTypeObject __pyx_FusedFunctionType_type = { #if PY_VERSION_HEX >= 0x030800b1 0, #endif +#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, +#endif }; static int __pyx_FusedFunction_init(void) { + __pyx_FusedFunctionType_type.tp_base = __pyx_CyFunctionType; __pyx_FusedFunctionType = __Pyx_FetchCommonType(&__pyx_FusedFunctionType_type); if (__pyx_FusedFunctionType == NULL) { return -1; @@ -59549,7 +59304,7 @@ static int __pyx_FusedFunction_init(void) { /* CLineInTraceback */ #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { +static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int c_line) { PyObject *use_cline; PyObject *ptype, *pvalue, *ptraceback; #if CYTHON_COMPILING_IN_CPYTHON @@ -59653,7 +59408,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } @@ -59757,7 +59512,6 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); @@ -59771,7 +59525,6 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return; } if ((0)) {} - else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); view->obj = NULL; Py_DECREF(obj); } @@ -59916,6 +59669,7 @@ static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { + case '?': return "'bool'"; case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; @@ -59958,7 +59712,7 @@ static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { - case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); @@ -60042,7 +59796,7 @@ static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; - case 'B': case 'H': case 'I': case 'L': case 'Q': + case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); @@ -60186,9 +59940,7 @@ static PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->ndim; -; + int i = 0, number, ndim; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, @@ -60196,6 +59948,7 @@ __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ndim = ctx->head->field->type->ndim; while (*ts && *ts != ')') { switch (*ts) { case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; @@ -60321,12 +60074,12 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha return NULL; } CYTHON_FALLTHROUGH; - case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 'p': - if (ctx->enc_type == *ts && got_Z == ctx->is_complex && - ctx->enc_packmode == ctx->new_packmode) { + if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && + (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { ctx->enc_count += ctx->new_count; ctx->new_count = 1; got_Z = 0; @@ -60412,13 +60165,13 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) if (buf->strides) { if (spec & __Pyx_MEMVIEW_CONTIG) { if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (buf->strides[dim] != sizeof(void *)) { + if (unlikely(buf->strides[dim] != sizeof(void *))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly contiguous " "in dimension %d.", dim); goto fail; } - } else if (buf->strides[dim] != buf->itemsize) { + } else if (unlikely(buf->strides[dim] != buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -60429,7 +60182,7 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) Py_ssize_t stride = buf->strides[dim]; if (stride < 0) stride = -stride; - if (stride < buf->itemsize) { + if (unlikely(stride < buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -60437,17 +60190,17 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) } } } else { - if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not contiguous in " "dimension %d", dim); goto fail; - } else if (spec & (__Pyx_MEMVIEW_PTR)) { + } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not indirect in " "dimension %d", dim); goto fail; - } else if (buf->suboffsets) { + } else if (unlikely(buf->suboffsets)) { PyErr_SetString(PyExc_ValueError, "Buffer exposes suboffsets but no strides"); goto fail; @@ -60461,7 +60214,7 @@ static int __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) { if (spec & __Pyx_MEMVIEW_DIRECT) { - if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { PyErr_Format(PyExc_ValueError, "Buffer not compatible with direct access " "in dimension %d.", dim); @@ -60469,7 +60222,7 @@ __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec } } if (spec & __Pyx_MEMVIEW_PTR) { - if (!buf->suboffsets || (buf->suboffsets[dim] < 0)) { + if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly accessible " "in dimension %d.", dim); @@ -60487,9 +60240,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) if (c_or_f_flag & __Pyx_IS_F_CONTIG) { Py_ssize_t stride = 1; for (i = 0; i < ndim; i++) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) - { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not fortran contiguous."); goto fail; @@ -60499,8 +60250,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { Py_ssize_t stride = 1; for (i = ndim - 1; i >- 1; i--) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not C contiguous."); goto fail; @@ -60541,7 +60291,7 @@ static int __Pyx_ValidateAndInit_memviewslice( goto fail; } buf = &memview->view; - if (buf->ndim != ndim) { + if (unlikely(buf->ndim != ndim)) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", ndim, buf->ndim); @@ -60549,9 +60299,9 @@ static int __Pyx_ValidateAndInit_memviewslice( } if (new_memview) { __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; } - if ((unsigned) buf->itemsize != dtype->size) { + if (unlikely((unsigned) buf->itemsize != dtype->size)) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", @@ -60564,12 +60314,12 @@ static int __Pyx_ValidateAndInit_memviewslice( } for (i = 0; i < ndim; i++) { spec = axes_specs[i]; - if (!__pyx_check_strides(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) goto fail; - if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) goto fail; } - if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) goto fail; if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, new_memview != NULL) == -1)) { @@ -61490,7 +61240,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_uint64_t(const char case 1: return a; case 2: - z = __Pyx_c_prod_float(a, a); return __Pyx_c_prod_float(a, a); case 3: z = __Pyx_c_prod_float(a, a); @@ -61645,7 +61394,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_uint64_t(const char case 1: return a; case 2: - z = __Pyx_c_prod_double(a, a); return __Pyx_c_prod_double(a, a); case 3: z = __Pyx_c_prod_double(a, a); @@ -61763,7 +61511,7 @@ __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, struct __pyx_memoryview_obj *memview_obj = NULL; __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); for (i = 0; i < ndim; i++) { - if (from_mvs->suboffsets[i] >= 0) { + if (unlikely(from_mvs->suboffsets[i] >= 0)) { PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " "indirect dimensions (axis %d)", i); goto fail; diff --git a/allel/opt/stats.c b/allel/opt/stats.c index 020f683b..06f6fc22 100644 --- a/allel/opt/stats.c +++ b/allel/opt/stats.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.29.10 */ +/* Generated by Cython 0.29.20 */ /* BEGIN: Cython Metadata { @@ -20,8 +20,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_10" -#define CYTHON_HEX_VERSION 0x001D0AF0 +#define CYTHON_ABI "0_29_20" +#define CYTHON_HEX_VERSION 0x001D14F0 #define CYTHON_FUTURE_DIVISION 1 #include #ifndef offsetof @@ -323,12 +323,12 @@ END: Cython Metadata */ #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" -#if PY_VERSION_HEX < 0x030800A4 +#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2 #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #define __Pyx_DefaultClassType PyType_Type #endif @@ -497,8 +497,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact +#ifndef PyObject_Unicode #define PyObject_Unicode PyObject_Str #endif +#endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) @@ -509,6 +511,13 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif +#if PY_VERSION_HEX >= 0x030900A4 + #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) +#else + #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) +#endif #if CYTHON_ASSUME_SAFE_MACROS #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) #else @@ -589,11 +598,10 @@ static CYTHON_INLINE float __PYX_NAN() { #define __Pyx_truncl truncl #endif - +#define __PYX_MARK_ERR_POS(f_index, lineno) \ + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } #define __PYX_ERR(f_index, lineno, Ln_error) \ -{ \ - __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ -} + { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } #ifndef __PYX_EXTERN_C #ifdef __cplusplus @@ -610,6 +618,9 @@ static CYTHON_INLINE float __PYX_NAN() { #include #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" + + /* NumPy API declarations from "numpy/__init__.pxd" */ + #include #include #include "pythread.h" @@ -958,7 +969,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":697 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -967,7 +978,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":698 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -976,7 +987,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":699 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -985,7 +996,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":700 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -994,7 +1005,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":704 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1003,7 +1014,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":705 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1012,7 +1023,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":706 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1021,7 +1032,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":707 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1030,7 +1041,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":711 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1039,7 +1050,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":712 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1048,7 +1059,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":721 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1057,7 +1068,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":722 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1066,7 +1077,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":723 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1075,7 +1086,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":725 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1084,7 +1095,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":726 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1093,7 +1104,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":727 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1102,7 +1113,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":729 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1111,7 +1122,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":730 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1120,7 +1131,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":732 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1129,7 +1140,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":733 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1138,7 +1149,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":734 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1177,7 +1188,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":736 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1186,7 +1197,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":737 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1195,7 +1206,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":738 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1204,7 +1215,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../pyenv/scikit-allel-py37/lib/python3.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 +/* "../../../pyenv/scikit-allel-dev/lib/python3.8/site-packages/numpy/__init__.pxd":740 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1496,7 +1507,7 @@ struct __pyx_memoryview_obj { }; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -1547,7 +1558,7 @@ struct __pyx_vtabstruct_memoryview { static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; -/* "View.MemoryView":961 +/* "View.MemoryView":965 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -1970,7 +1981,7 @@ static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); #define __Pyx_PyFunction_FastCall(func, args, nargs)\ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); #else #define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) #endif @@ -2137,7 +2148,7 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -2154,7 +2165,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -2334,6 +2345,9 @@ static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_nam /* SetVTable.proto */ static int __Pyx_SetVtable(PyObject *dict, void *vtable); +/* PyObjectGetAttrStrNoError.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); + /* SetupReduce.proto */ static int __Pyx_setup_reduce(PyObject* type_obj); @@ -2351,7 +2365,7 @@ static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, /* FetchCommonType.proto */ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); -/* CythonFunction.proto */ +/* CythonFunctionShared.proto */ #define __Pyx_CyFunction_USED 1 #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 @@ -2379,6 +2393,7 @@ typedef struct { PyObject *func_classobj; void *defaults; int defaults_pyobjects; + size_t defaults_size; // used by FusedFunction for copying defaults int flags; PyObject *defaults_tuple; PyObject *defaults_kwdict; @@ -2387,9 +2402,7 @@ typedef struct { } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; #define __Pyx_CyFunction_Check(obj) (__Pyx_TypeCheck(obj, __pyx_CyFunctionType)) -#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ - __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) -static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *self, PyObject *module, PyObject *globals, @@ -2412,11 +2425,8 @@ typedef struct { PyObject *type; PyObject *self; } __pyx_FusedFunctionObject; -#define __pyx_FusedFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ - __pyx_FusedFunction_New(__pyx_FusedFunctionType, ml, flags, qualname, self, module, globals, code) -static PyObject *__pyx_FusedFunction_New(PyTypeObject *type, - PyMethodDef *ml, int flags, - PyObject *qualname, PyObject *self, +static PyObject *__pyx_FusedFunction_New(PyMethodDef *ml, int flags, + PyObject *qualname, PyObject *closure, PyObject *module, PyObject *globals, PyObject *code); static int __pyx_FusedFunction_clear(__pyx_FusedFunctionObject *self); @@ -3217,7 +3227,6 @@ static const char __pyx_k_gn_pairwise_corrcoef_int8[] = "gn_pairwise_corrcoef_in static const char __pyx_k_gn_pairwise2_corrcoef_int8[] = "gn_pairwise2_corrcoef_int8"; static const char __pyx_k_No_matching_signature_found[] = "No matching signature found"; static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static const char __pyx_k_phase_parents_by_transmission[] = "phase_parents_by_transmission"; static const char __pyx_k_phase_progeny_by_transmission[] = "phase_progeny_by_transmission"; static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; @@ -3265,7 +3274,6 @@ static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; static const char __pyx_k_pyx_fuse_0neighbour_shared_pre_2[] = "__pyx_fuse_0neighbour_shared_prefix_lengths_unsorted"; @@ -3429,8 +3437,6 @@ static PyObject *__pyx_n_s_n_variants; static PyObject *__pyx_n_s_name; static PyObject *__pyx_n_s_name_2; static PyObject *__pyx_n_s_nan; -static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; -static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_ndim; static PyObject *__pyx_n_s_neighbour_shared_prefix_lengths; static PyObject *__pyx_n_s_neighbour_shared_prefix_lengths_2; @@ -3731,8 +3737,6 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_280state_transitions(CYTHON_UNUSED static PyObject *__pyx_pf_5allel_3opt_5stats_282state_transitions(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_x, PyObject *__pyx_v_states); /* proto */ static PyObject *__pyx_pf_5allel_3opt_5stats_284state_transitions(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_x, PyObject *__pyx_v_states); /* proto */ static PyObject *__pyx_pf_5allel_3opt_5stats_286state_transitions(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_x, PyObject *__pyx_v_states); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ @@ -3792,7 +3796,7 @@ static PyObject *__pyx_k__12; static PyObject *__pyx_codeobj_; static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; -static PyObject *__pyx_slice__35; +static PyObject *__pyx_slice__33; static PyObject *__pyx_tuple__13; static PyObject *__pyx_tuple__14; static PyObject *__pyx_tuple__15; @@ -3813,14 +3817,13 @@ static PyObject *__pyx_tuple__29; static PyObject *__pyx_tuple__30; static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__32; -static PyObject *__pyx_tuple__33; static PyObject *__pyx_tuple__34; +static PyObject *__pyx_tuple__35; static PyObject *__pyx_tuple__36; -static PyObject *__pyx_tuple__37; static PyObject *__pyx_tuple__38; +static PyObject *__pyx_tuple__39; static PyObject *__pyx_tuple__40; static PyObject *__pyx_tuple__41; -static PyObject *__pyx_tuple__42; static PyObject *__pyx_tuple__43; static PyObject *__pyx_tuple__45; static PyObject *__pyx_tuple__47; @@ -3835,15 +3838,15 @@ static PyObject *__pyx_tuple__63; static PyObject *__pyx_tuple__65; static PyObject *__pyx_tuple__67; static PyObject *__pyx_tuple__69; +static PyObject *__pyx_tuple__70; static PyObject *__pyx_tuple__71; static PyObject *__pyx_tuple__72; static PyObject *__pyx_tuple__73; static PyObject *__pyx_tuple__74; -static PyObject *__pyx_tuple__75; -static PyObject *__pyx_tuple__76; static PyObject *__pyx_codeobj__2; static PyObject *__pyx_codeobj__3; -static PyObject *__pyx_codeobj__39; +static PyObject *__pyx_codeobj__37; +static PyObject *__pyx_codeobj__42; static PyObject *__pyx_codeobj__44; static PyObject *__pyx_codeobj__46; static PyObject *__pyx_codeobj__48; @@ -3857,7 +3860,6 @@ static PyObject *__pyx_codeobj__62; static PyObject *__pyx_codeobj__64; static PyObject *__pyx_codeobj__66; static PyObject *__pyx_codeobj__68; -static PyObject *__pyx_codeobj__70; /* Late includes */ /* "allel/opt/stats.pyx":40 @@ -3888,11 +3890,11 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr Py_ssize_t __pyx_t_2; Py_ssize_t __pyx_t_3; Py_ssize_t __pyx_t_4; - Py_ssize_t __pyx_t_5; + int __pyx_t_5; int __pyx_t_6; - int __pyx_t_7; - Py_ssize_t __pyx_t_8; - Py_ssize_t __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_TraceCall("gn_corrcoef_int8", __pyx_f[0], 40, 1, __PYX_ERR(0, 40, __pyx_L1_error)); /* "allel/opt/stats.pyx":51 @@ -3938,8 +3940,8 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr * # consider negative values as missing * if x >= 0 and y >= 0: */ - __pyx_t_5 = __pyx_v_i; - __pyx_v_y = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn1.data + __pyx_t_5 * __pyx_v_gn1.strides[0]) ))); + __pyx_t_4 = __pyx_v_i; + __pyx_v_y = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn1.data + __pyx_t_4 * __pyx_v_gn1.strides[0]) ))); /* "allel/opt/stats.pyx":58 * y = gn1[i] @@ -3948,16 +3950,16 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr * n += 1 * m0 += x */ - __pyx_t_7 = ((__pyx_v_x >= 0) != 0); - if (__pyx_t_7) { + __pyx_t_6 = ((__pyx_v_x >= 0) != 0); + if (__pyx_t_6) { } else { - __pyx_t_6 = __pyx_t_7; + __pyx_t_5 = __pyx_t_6; goto __pyx_L6_bool_binop_done; } - __pyx_t_7 = ((__pyx_v_y >= 0) != 0); - __pyx_t_6 = __pyx_t_7; + __pyx_t_6 = ((__pyx_v_y >= 0) != 0); + __pyx_t_5 = __pyx_t_6; __pyx_L6_bool_binop_done:; - if (__pyx_t_6) { + if (__pyx_t_5) { /* "allel/opt/stats.pyx":59 * # consider negative values as missing @@ -3993,8 +3995,8 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr * ysq = gn1_sq[i] * v0 += xsq */ - __pyx_t_8 = __pyx_v_i; - __pyx_v_xsq = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn0_sq.data + __pyx_t_8 * __pyx_v_gn0_sq.strides[0]) ))); + __pyx_t_4 = __pyx_v_i; + __pyx_v_xsq = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn0_sq.data + __pyx_t_4 * __pyx_v_gn0_sq.strides[0]) ))); /* "allel/opt/stats.pyx":63 * m1 += y @@ -4003,8 +4005,8 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr * v0 += xsq * v1 += ysq */ - __pyx_t_9 = __pyx_v_i; - __pyx_v_ysq = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn1_sq.data + __pyx_t_9 * __pyx_v_gn1_sq.strides[0]) ))); + __pyx_t_4 = __pyx_v_i; + __pyx_v_ysq = (*((__pyx_t_5numpy_int8_t *) ( /* dim=0 */ (__pyx_v_gn1_sq.data + __pyx_t_4 * __pyx_v_gn1_sq.strides[0]) ))); /* "allel/opt/stats.pyx":64 * xsq = gn0_sq[i] @@ -4050,22 +4052,22 @@ static CYTHON_INLINE __pyx_t_5numpy_float32_t __pyx_f_5allel_3opt_5stats_gn_corr * return nan32 * */ - __pyx_t_7 = ((__pyx_v_n == 0) != 0); - if (!__pyx_t_7) { + __pyx_t_6 = ((__pyx_v_n == 0) != 0); + if (!__pyx_t_6) { } else { - __pyx_t_6 = __pyx_t_7; + __pyx_t_5 = __pyx_t_6; goto __pyx_L9_bool_binop_done; } - __pyx_t_7 = ((__pyx_v_v0 == 0.0) != 0); - if (!__pyx_t_7) { + __pyx_t_6 = ((__pyx_v_v0 == 0.0) != 0); + if (!__pyx_t_6) { } else { - __pyx_t_6 = __pyx_t_7; + __pyx_t_5 = __pyx_t_6; goto __pyx_L9_bool_binop_done; } - __pyx_t_7 = ((__pyx_v_v1 == 0.0) != 0); - __pyx_t_6 = __pyx_t_7; + __pyx_t_6 = ((__pyx_v_v1 == 0.0) != 0); + __pyx_t_5 = __pyx_t_6; __pyx_L9_bool_binop_done:; - if (__pyx_t_6) { + if (__pyx_t_5) { /* "allel/opt/stats.pyx":70 * # early out @@ -4201,6 +4203,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_1gn_corrcoef_int8(PyObject *__pyx_s __Pyx_memviewslice __pyx_v_gn1 = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_gn0_sq = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_gn1_sq = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("gn_corrcoef_int8 (wrapper)", 0); @@ -4282,6 +4287,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_gn_corrcoef_int8(CYTHON_UNUSED PyOb __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("gn_corrcoef_int8", 0); __Pyx_TraceCall("gn_corrcoef_int8 (wrapper)", __pyx_f[0], 40, 0, __PYX_ERR(0, 40, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -4324,6 +4332,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_3gn_pairwise_corrcoef_int8(PyObject static PyMethodDef __pyx_mdef_5allel_3opt_5stats_3gn_pairwise_corrcoef_int8 = {"gn_pairwise_corrcoef_int8", (PyCFunction)__pyx_pw_5allel_3opt_5stats_3gn_pairwise_corrcoef_int8, METH_O, 0}; static PyObject *__pyx_pw_5allel_3opt_5stats_3gn_pairwise_corrcoef_int8(PyObject *__pyx_self, PyObject *__pyx_arg_gn) { __Pyx_memviewslice __pyx_v_gn = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("gn_pairwise_corrcoef_int8 (wrapper)", 0); @@ -4382,6 +4393,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_2gn_pairwise_corrcoef_int8(CYTHON_U Py_ssize_t __pyx_t_14; __Pyx_memviewslice __pyx_t_15 = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_t_16; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_TraceFrameInit(__pyx_codeobj_) __Pyx_RefNannySetupContext("gn_pairwise_corrcoef_int8", 0); __Pyx_TraceCall("gn_pairwise_corrcoef_int8", __pyx_f[0], 90, 0, __PYX_ERR(0, 90, __pyx_L1_error)); @@ -4571,7 +4585,6 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_2gn_pairwise_corrcoef_int8(CYTHON_U { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 113, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -4597,7 +4610,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 114, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -4623,7 +4635,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn_sq.strides[0]; - if ((0)) __PYX_ERR(0, 115, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -4649,7 +4660,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn_sq.strides[0]; - if ((0)) __PYX_ERR(0, 116, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -4708,13 +4718,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); #endif goto __pyx_L5; } - __pyx_L4_error: { - #ifdef WITH_THREAD - __Pyx_FastGIL_Forget(); - Py_BLOCK_THREADS - #endif - goto __pyx_L1_error; - } __pyx_L5:; } } @@ -4802,6 +4805,9 @@ static PyMethodDef __pyx_mdef_5allel_3opt_5stats_5gn_pairwise2_corrcoef_int8 = { static PyObject *__pyx_pw_5allel_3opt_5stats_5gn_pairwise2_corrcoef_int8(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { __Pyx_memviewslice __pyx_v_gna = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_gnb = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("gn_pairwise2_corrcoef_int8 (wrapper)", 0); @@ -4901,6 +4907,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_4gn_pairwise2_corrcoef_int8(CYTHON_ __Pyx_memviewslice __pyx_t_15 = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_TraceFrameInit(__pyx_codeobj__2) __Pyx_RefNannySetupContext("gn_pairwise2_corrcoef_int8", 0); __Pyx_TraceCall("gn_pairwise2_corrcoef_int8", __pyx_f[0], 126, 0, __PYX_ERR(0, 126, __pyx_L1_error)); @@ -5158,7 +5167,6 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_4gn_pairwise2_corrcoef_int8(CYTHON_ { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gna.strides[0]; - if ((0)) __PYX_ERR(0, 149, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -5184,7 +5192,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gnb.strides[0]; - if ((0)) __PYX_ERR(0, 150, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -5210,7 +5217,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gna_sq.strides[0]; - if ((0)) __PYX_ERR(0, 151, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -5236,7 +5242,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gnb_sq.strides[0]; - if ((0)) __PYX_ERR(0, 152, __pyx_L4_error) __pyx_t_15.data += __pyx_tmp_idx * __pyx_tmp_stride; } @@ -5287,13 +5292,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); #endif goto __pyx_L5; } - __pyx_L4_error: { - #ifdef WITH_THREAD - __Pyx_FastGIL_Forget(); - Py_BLOCK_THREADS - #endif - goto __pyx_L1_error; - } __pyx_L5:; } } @@ -5386,6 +5384,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_7gn_locate_unlinked_int8(PyObject * Py_ssize_t __pyx_v_size; Py_ssize_t __pyx_v_step; __pyx_t_5numpy_float32_t __pyx_v_threshold; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("gn_locate_unlinked_int8 (wrapper)", 0); @@ -5517,12 +5518,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_6gn_locate_unlinked_int8(CYTHON_UNU Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - __Pyx_memviewslice __pyx_t_19 = { 0, 0, { 0 }, { 0 }, { 0 } }; - Py_ssize_t __pyx_t_20; - Py_ssize_t __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; + __Pyx_memviewslice __pyx_t_18 = { 0, 0, { 0 }, { 0 }, { 0 } }; + Py_ssize_t __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_TraceFrameInit(__pyx_codeobj__3) __Pyx_RefNannySetupContext("gn_locate_unlinked_int8", 0); __Pyx_TraceCall("gn_locate_unlinked_int8", __pyx_f[0], 161, 0, __PYX_ERR(0, 161, __pyx_L1_error)); @@ -5803,8 +5803,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_6gn_locate_unlinked_int8(CYTHON_UNU * gn0 = gn[i] * gn1 = gn[j] */ - __pyx_t_18 = __pyx_v_j; - __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_18 * __pyx_v_loc.strides[0]) ))) != 0); + __pyx_t_14 = __pyx_v_j; + __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_14 * __pyx_v_loc.strides[0]) ))) != 0); if (__pyx_t_11) { /* "allel/opt/stats.pyx":197 @@ -5814,24 +5814,23 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_6gn_locate_unlinked_int8(CYTHON_UNU * gn1 = gn[j] * gn0_sq = gn_sq[i] */ - __pyx_t_19.data = __pyx_v_gn.data; - __pyx_t_19.memview = __pyx_v_gn.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn.data; + __pyx_t_18.memview = __pyx_v_gn.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 197, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); - __pyx_v_gn0 = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn0 = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":198 * if loc[j]: @@ -5840,24 +5839,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); * gn0_sq = gn_sq[i] * gn1_sq = gn_sq[j] */ - __pyx_t_19.data = __pyx_v_gn.data; - __pyx_t_19.memview = __pyx_v_gn.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn.data; + __pyx_t_18.memview = __pyx_v_gn.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 198, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); - __pyx_v_gn1 = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn1 = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":199 * gn0 = gn[i] @@ -5866,24 +5864,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); * gn1_sq = gn_sq[j] * r_squared = gn_corrcoef_int8(gn0, gn1, gn0_sq, gn1_sq) ** 2 */ - __pyx_t_19.data = __pyx_v_gn_sq.data; - __pyx_t_19.memview = __pyx_v_gn_sq.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn_sq.data; + __pyx_t_18.memview = __pyx_v_gn_sq.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn_sq.strides[0]; - if ((0)) __PYX_ERR(0, 199, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn_sq.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn_sq.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn_sq.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn_sq.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); - __pyx_v_gn0_sq = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn0_sq = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":200 * gn1 = gn[j] @@ -5892,24 +5889,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); * r_squared = gn_corrcoef_int8(gn0, gn1, gn0_sq, gn1_sq) ** 2 * if r_squared > threshold: */ - __pyx_t_19.data = __pyx_v_gn_sq.data; - __pyx_t_19.memview = __pyx_v_gn_sq.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn_sq.data; + __pyx_t_18.memview = __pyx_v_gn_sq.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn_sq.strides[0]; - if ((0)) __PYX_ERR(0, 200, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn_sq.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn_sq.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn_sq.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn_sq.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); - __pyx_v_gn1_sq = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn1_sq = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":201 * gn0_sq = gn_sq[i] @@ -5937,8 +5933,8 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); * * else: */ - __pyx_t_20 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_20 * __pyx_v_loc.strides[0]) )) = 0; + __pyx_t_14 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_14 * __pyx_v_loc.strides[0]) )) = 0; /* "allel/opt/stats.pyx":202 * gn1_sq = gn_sq[j] @@ -5999,8 +5995,8 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); * # don't recalculate anything from overlap with previous * # window */ - __pyx_t_21 = __pyx_v_i; - __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_21 * __pyx_v_loc.strides[0]) ))) != 0); + __pyx_t_19 = __pyx_v_i; + __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_19 * __pyx_v_loc.strides[0]) ))) != 0); if (__pyx_t_11) { /* "allel/opt/stats.pyx":212 @@ -6048,8 +6044,8 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); * gn0 = gn[i] * gn1 = gn[j] */ - __pyx_t_22 = __pyx_v_j; - __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_22 * __pyx_v_loc.strides[0]) ))) != 0); + __pyx_t_19 = __pyx_v_j; + __pyx_t_11 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_19 * __pyx_v_loc.strides[0]) ))) != 0); if (__pyx_t_11) { /* "allel/opt/stats.pyx":217 @@ -6059,24 +6055,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); * gn1 = gn[j] * gn0_sq = gn_sq[i] */ - __pyx_t_19.data = __pyx_v_gn.data; - __pyx_t_19.memview = __pyx_v_gn.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn.data; + __pyx_t_18.memview = __pyx_v_gn.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 217, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); - __pyx_v_gn0 = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn0 = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":218 * if loc[j]: @@ -6085,24 +6080,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0, 0); * gn0_sq = gn_sq[i] * gn1_sq = gn_sq[j] */ - __pyx_t_19.data = __pyx_v_gn.data; - __pyx_t_19.memview = __pyx_v_gn.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn.data; + __pyx_t_18.memview = __pyx_v_gn.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn.strides[0]; - if ((0)) __PYX_ERR(0, 218, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); - __pyx_v_gn1 = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn1 = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":219 * gn0 = gn[i] @@ -6111,24 +6105,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1, 0); * gn1_sq = gn_sq[j] * r_squared = gn_corrcoef_int8(gn0, gn1, gn0_sq, gn1_sq) ** 2 */ - __pyx_t_19.data = __pyx_v_gn_sq.data; - __pyx_t_19.memview = __pyx_v_gn_sq.memview; - __PYX_INC_MEMVIEW(&__pyx_t_19, 0); + __pyx_t_18.data = __pyx_v_gn_sq.data; + __pyx_t_18.memview = __pyx_v_gn_sq.memview; + __PYX_INC_MEMVIEW(&__pyx_t_18, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_gn_sq.strides[0]; - if ((0)) __PYX_ERR(0, 219, __pyx_L8_error) - __pyx_t_19.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_18.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_19.shape[0] = __pyx_v_gn_sq.shape[1]; -__pyx_t_19.strides[0] = __pyx_v_gn_sq.strides[1]; - __pyx_t_19.suboffsets[0] = -1; +__pyx_t_18.shape[0] = __pyx_v_gn_sq.shape[1]; +__pyx_t_18.strides[0] = __pyx_v_gn_sq.strides[1]; + __pyx_t_18.suboffsets[0] = -1; __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); - __pyx_v_gn0_sq = __pyx_t_19; - __pyx_t_19.memview = NULL; - __pyx_t_19.data = NULL; + __pyx_v_gn0_sq = __pyx_t_18; + __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":220 * gn1 = gn[j] @@ -6137,24 +6130,23 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn0_sq, 0); 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+ __pyx_t_18.memview = NULL; + __pyx_t_18.data = NULL; /* "allel/opt/stats.pyx":221 * gn0_sq = gn_sq[i] @@ -6182,8 +6174,8 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); * * if last: */ - __pyx_t_23 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_23 * __pyx_v_loc.strides[0]) )) = 0; + __pyx_t_19 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_loc.data + __pyx_t_19 * __pyx_v_loc.strides[0]) )) = 0; /* "allel/opt/stats.pyx":222 * gn1_sq = gn_sq[j] @@ -6276,13 +6268,6 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); #endif goto __pyx_L4_break; } - __pyx_L8_error: { - #ifdef WITH_THREAD - __Pyx_FastGIL_Forget(); - Py_BLOCK_THREADS - #endif - goto __pyx_L1_error; - } __pyx_L9:; } } @@ -6316,7 +6301,7 @@ __PYX_XDEC_MEMVIEW(&__pyx_v_gn1_sq, 0); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_6); __PYX_XDEC_MEMVIEW(&__pyx_t_7, 1); - __PYX_XDEC_MEMVIEW(&__pyx_t_19, 1); + __PYX_XDEC_MEMVIEW(&__pyx_t_18, 1); __Pyx_AddTraceback("allel.opt.stats.gn_locate_unlinked_int8", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -6350,6 +6335,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_9shared_prefix_length(PyObject *__p PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -6471,6 +6459,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_8shared_prefix_length(CYTHON_UNUSED Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("shared_prefix_length", 0); __Pyx_TraceCall("shared_prefix_length", __pyx_f[0], 231, 0, __PYX_ERR(0, 231, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -7180,6 +7171,9 @@ static Py_ssize_t __pyx_fuse_0__pyx_f_5allel_3opt_5stats_shared_prefix_length(__ Py_ssize_t __pyx_t_4; Py_ssize_t __pyx_t_5; 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{ Py_ssize_t __pyx_tmp_idx = __pyx_v_ix; Py_ssize_t __pyx_tmp_stride = __pyx_v_h.strides[1]; - if ((0)) __PYX_ERR(0, 321, __pyx_L4_error) __pyx_t_5.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_11.data = __pyx_v_h.data; - __pyx_t_11.memview = __pyx_v_h.memview; - __PYX_INC_MEMVIEW(&__pyx_t_11, 0); - __pyx_t_11.shape[0] = __pyx_v_h.shape[0]; -__pyx_t_11.strides[0] = __pyx_v_h.strides[0]; - __pyx_t_11.suboffsets[0] = -1; +__pyx_t_10.data = __pyx_v_h.data; + __pyx_t_10.memview = __pyx_v_h.memview; + __PYX_INC_MEMVIEW(&__pyx_t_10, 0); + __pyx_t_10.shape[0] = __pyx_v_h.shape[0]; +__pyx_t_10.strides[0] = __pyx_v_h.strides[0]; + __pyx_t_10.suboffsets[0] = -1; { Py_ssize_t __pyx_tmp_idx = __pyx_v_jx; Py_ssize_t __pyx_tmp_stride = __pyx_v_h.strides[1]; - if ((0)) __PYX_ERR(0, 321, __pyx_L4_error) - __pyx_t_11.data += __pyx_tmp_idx * __pyx_tmp_stride; + __pyx_t_10.data += __pyx_tmp_idx * __pyx_tmp_stride; } -__pyx_t_12 = __pyx_v_i; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_lengths.data + __pyx_t_12 * __pyx_v_lengths.strides[0]) )) = __pyx_fuse_2__pyx_f_5allel_3opt_5stats_shared_prefix_length(__pyx_t_5, __pyx_t_11, 0); 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__pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -33759,15 +33904,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_0ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -33951,9 +34094,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -33962,22 +34105,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -34006,8 +34149,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -34018,8 +34161,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -34037,8 +34180,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -34067,11 +34210,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -34080,8 +34223,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_146ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -34175,6 +34318,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_308__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -34224,6 +34370,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_149ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -34348,15 +34497,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_1ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -34540,9 +34687,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -34551,22 +34698,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -34595,8 +34742,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -34607,8 +34754,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -34626,8 +34773,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -34656,11 +34803,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -34669,8 +34816,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_148ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -34764,6 +34911,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_310__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -34813,6 +34963,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_151ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -34937,15 +35090,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_2ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -35129,9 +35280,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -35140,22 +35291,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -35184,8 +35335,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -35196,8 +35347,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -35215,8 +35366,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -35245,11 +35396,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -35258,8 +35409,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_150ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -35353,6 +35504,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_312__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -35402,6 +35556,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_153ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -35526,15 +35683,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_3ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -35718,9 +35873,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -35729,22 +35884,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -35773,8 +35928,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -35785,8 +35940,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -35804,8 +35959,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -35834,11 +35989,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -35847,8 +36002,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_152ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -35942,6 +36097,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_314__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -35991,6 +36149,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_155ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -36115,15 +36276,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_4ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -36307,9 +36466,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -36318,22 +36477,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -36362,8 +36521,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -36374,8 +36533,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -36393,8 +36552,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -36423,11 +36582,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -36436,8 +36595,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_154ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -36531,6 +36690,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_316__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -36580,6 +36742,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_157ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -36704,15 +36869,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_5ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -36896,9 +37059,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -36907,22 +37070,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -36951,8 +37114,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -36963,8 +37126,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -36982,8 +37145,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -37012,11 +37175,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -37025,8 +37188,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_156ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -37120,6 +37283,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_318__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -37169,6 +37335,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_159ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -37293,15 +37462,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_6ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -37485,9 +37652,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -37496,22 +37663,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -37540,8 +37707,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -37552,8 +37719,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -37571,8 +37738,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -37601,11 +37768,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -37614,8 +37781,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_158ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -37709,6 +37876,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_320__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -37758,6 +37928,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_161ihh_scan(PyObject *_ __Pyx_memviewslice __pyx_v_gaps = { 0, 0, { 0 }, { 0 }, { 0 } }; __pyx_t_5numpy_float64_t __pyx_v_min_ehh; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh_scan (wrapper)", 0); @@ -37882,15 +38055,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - __pyx_t_5numpy_float64_t __pyx_t_24; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_25; - Py_ssize_t __pyx_t_26; + int __pyx_t_18; + int __pyx_t_19; + __pyx_t_5numpy_float64_t __pyx_t_20; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_21; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7ihh_scan", 0); __Pyx_TraceCall("__pyx_fuse_7ihh_scan", __pyx_f[0], 538, 0, __PYX_ERR(0, 538, __pyx_L1_error)); @@ -38074,9 +38245,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":578 * a2 = h[i, k] # allele on second haplotype in pair @@ -38085,22 +38256,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":580 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -38129,8 +38300,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * # increment pair index */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -38141,8 +38312,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * # increment pair index * u += 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":586 * ssl[u] = l @@ -38160,8 +38331,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * l_max = l * */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":589 * # update max l @@ -38190,11 +38361,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_25.__pyx_n = 2; - __pyx_t_25.min_ehh = __pyx_v_min_ehh; - __pyx_t_25.include_edges = __pyx_v_include_edges; - __pyx_t_24 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_25); - __pyx_v_ihh = __pyx_t_24; + __pyx_t_21.__pyx_n = 2; + __pyx_t_21.min_ehh = __pyx_v_min_ehh; + __pyx_t_21.include_edges = __pyx_v_include_edges; + __pyx_t_20 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_v_ssl, __pyx_v_l_max, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_21); + __pyx_v_ihh = __pyx_t_20; /* "allel/opt/stats.pyx":595 * min_ehh=min_ehh, @@ -38203,8 +38374,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_160ihh_scan(CYTHON_UNUSED PyObject * * return np.asarray(vihh) */ - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_26 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vihh.data + __pyx_t_14 * __pyx_v_vihh.strides[0]) )) = __pyx_v_ihh; } } @@ -38308,6 +38479,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_25nsl_scan(PyObject *__pyx_self, Py PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -38429,6 +38603,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_24nsl_scan(CYTHON_UNUSED PyObject * Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("nsl_scan", 0); __Pyx_TraceCall("nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -39130,6 +39307,9 @@ static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_165nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_0__pyx_mdef_5allel_3opt_5stats_165nsl_scan = {"__pyx_fuse_0nsl_scan", (PyCFunction)__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_165nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_165nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -39184,13 +39364,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_0nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -39374,9 +39552,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -39385,22 +39563,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -39429,8 +39607,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -39441,8 +39619,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -39490,8 +39668,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_164nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -39589,6 +39767,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_167nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_1__pyx_mdef_5allel_3opt_5stats_167nsl_scan = {"__pyx_fuse_1nsl_scan", (PyCFunction)__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_167nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_167nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -39643,13 +39824,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_1nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -39833,9 +40012,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -39844,22 +40023,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -39888,8 +40067,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -39900,8 +40079,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -39949,8 +40128,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_166nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -40048,6 +40227,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_169nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_2__pyx_mdef_5allel_3opt_5stats_169nsl_scan = {"__pyx_fuse_2nsl_scan", (PyCFunction)__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_169nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_169nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -40102,13 +40284,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_2nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -40292,9 +40472,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -40303,22 +40483,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -40347,8 +40527,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -40359,8 +40539,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -40408,8 +40588,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_168nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -40507,6 +40687,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_171nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_3__pyx_mdef_5allel_3opt_5stats_171nsl_scan = {"__pyx_fuse_3nsl_scan", (PyCFunction)__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_171nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_171nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -40561,13 +40744,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_3nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -40751,9 +40932,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -40762,22 +40943,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -40806,8 +40987,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -40818,8 +40999,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -40867,8 +41048,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_170nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -40966,6 +41147,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_173nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_4__pyx_mdef_5allel_3opt_5stats_173nsl_scan = {"__pyx_fuse_4nsl_scan", (PyCFunction)__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_173nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_173nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -41020,13 +41204,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_4nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -41210,9 +41392,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -41221,22 +41403,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -41265,8 +41447,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -41277,8 +41459,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -41326,8 +41508,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_172nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -41425,6 +41607,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_175nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_5__pyx_mdef_5allel_3opt_5stats_175nsl_scan = {"__pyx_fuse_5nsl_scan", (PyCFunction)__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_175nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_175nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -41479,13 +41664,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_5nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -41669,9 +41852,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -41680,22 +41863,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -41724,8 +41907,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -41736,8 +41919,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -41785,8 +41968,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_174nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -41884,6 +42067,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_177nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_6__pyx_mdef_5allel_3opt_5stats_177nsl_scan = {"__pyx_fuse_6nsl_scan", (PyCFunction)__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_177nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_177nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -41938,13 +42124,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_6nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -42128,9 +42312,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -42139,22 +42323,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -42183,8 +42367,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -42195,8 +42379,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -42244,8 +42428,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_176nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -42343,6 +42527,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_179nsl_scan(PyObject *_ static PyMethodDef __pyx_fuse_7__pyx_mdef_5allel_3opt_5stats_179nsl_scan = {"__pyx_fuse_7nsl_scan", (PyCFunction)__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_179nsl_scan, METH_O, __pyx_doc_5allel_3opt_5stats_24nsl_scan}; static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_179nsl_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl_scan (wrapper)", 0); @@ -42397,13 +42584,11 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; + int __pyx_t_18; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7nsl_scan", 0); __Pyx_TraceCall("__pyx_fuse_7nsl_scan", __pyx_f[0], 602, 0, __PYX_ERR(0, 602, __pyx_L1_error)); @@ -42587,9 +42772,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject * # test for non-equal and non-missing alleles * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":639 * a2 = h[i, k] # allele on second haplotype in pair @@ -42598,22 +42783,22 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject * # break shared suffix, reset length to zero * l = 0 */ - __pyx_t_21 = ((__pyx_v_a1 != __pyx_v_a2) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 != __pyx_v_a2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a1 >= 0) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 >= 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 >= 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":641 * if (a1 != a2) and (a1 >= 0) and (a2 >= 0): @@ -42642,8 +42827,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l */ /*else*/ { - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); } __pyx_L12:; @@ -42654,8 +42839,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject * ssl_sum += l * # increment pair index */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":646 * l = ssl[u] + 1 @@ -42703,8 +42888,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_178nsl_scan(CYTHON_UNUSED PyObject * * return np.asarray(vnsl) */ - __pyx_t_24 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_24 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vnsl.data + __pyx_t_14 * __pyx_v_vnsl.strides[0]) )) = __pyx_v_nsl; } } @@ -42814,6 +42999,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_27ssl01_scan(PyObject *__pyx_self, PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -42935,6 +43123,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_26ssl01_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("ssl01_scan", 0); __Pyx_TraceCall("ssl01_scan", __pyx_f[0], 659, 0, __PYX_ERR(0, 659, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -43638,6 +43829,9 @@ static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_183ssl01_scan(PyObject __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_v_stat = 0; PyObject *__pyx_v_kwargs = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ssl01_scan (wrapper)", 0); @@ -43738,24 +43932,20 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; + int __pyx_t_24; + __pyx_t_5numpy_float64_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; - int __pyx_t_31; - __pyx_t_5numpy_float64_t __pyx_t_32; - Py_ssize_t __pyx_t_33; - Py_ssize_t __pyx_t_34; - PyObject *__pyx_t_35 = NULL; + PyObject *__pyx_t_28 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0ssl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_0ssl01_scan", __pyx_f[0], 659, 0, __PYX_ERR(0, 659, __pyx_L1_error)); @@ -44031,9 +44221,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -44042,16 +44232,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -44060,8 +44250,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -44070,8 +44260,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; 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+ __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -44114,8 +44304,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -44124,8 +44314,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_182ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; 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/* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -44927,16 +45116,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -44945,8 +45134,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -44955,8 +45144,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -44975,12 +45164,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":701 * ssl[u] = l @@ -44989,8 +45178,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -44999,8 +45188,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -45009,8 +45198,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":704 * ssl[u] = l @@ -45038,12 +45227,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_184ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); 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- __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -45383,7 +45572,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -45408,6 +45597,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_187ssl01_scan(PyObject __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; 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- if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -45830,8 +46018,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_186ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -45840,8 +46028,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_186ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; 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+ __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -45884,8 +46072,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_186ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -45894,8 +46082,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_186ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; 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+ if (likely(__pyx_t_28)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); - __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -46268,7 +46456,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); 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+ __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -46725,8 +46912,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -46745,12 +46932,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":701 * ssl[u] = l @@ -46759,8 +46946,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -46769,8 +46956,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -46779,8 +46966,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":704 * ssl[u] = l @@ -46808,12 +46995,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_188ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); 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- __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -47153,7 +47340,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -47178,6 +47365,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_191ssl01_scan(PyObject __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_v_stat = 0; PyObject *__pyx_v_kwargs = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ssl01_scan (wrapper)", 0); @@ -47278,24 +47468,20 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; + int __pyx_t_24; + __pyx_t_5numpy_float64_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; - int __pyx_t_31; - __pyx_t_5numpy_float64_t __pyx_t_32; - Py_ssize_t __pyx_t_33; - Py_ssize_t __pyx_t_34; - PyObject *__pyx_t_35 = NULL; + PyObject *__pyx_t_28 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4ssl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_4ssl01_scan", __pyx_f[0], 659, 0, __PYX_ERR(0, 659, __pyx_L1_error)); @@ -47571,9 +47757,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -47582,16 +47768,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -47600,8 +47786,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -47610,8 +47796,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; 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+ __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -47654,8 +47840,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -47664,8 +47850,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_190ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; 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+ __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -48495,8 +48680,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -48515,12 +48700,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":701 * ssl[u] = l @@ -48529,8 +48714,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -48539,8 +48724,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -48549,8 +48734,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":704 * ssl[u] = l @@ -48578,12 +48763,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_192ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); 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- __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -48923,7 +49108,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -48948,6 +49133,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_195ssl01_scan(PyObject __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_v_stat = 0; PyObject *__pyx_v_kwargs = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ssl01_scan (wrapper)", 0); @@ -49048,24 +49236,20 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; + int __pyx_t_24; + __pyx_t_5numpy_float64_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; - int __pyx_t_31; - __pyx_t_5numpy_float64_t __pyx_t_32; - Py_ssize_t __pyx_t_33; - Py_ssize_t __pyx_t_34; - PyObject *__pyx_t_35 = NULL; + PyObject *__pyx_t_28 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6ssl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_6ssl01_scan", __pyx_f[0], 659, 0, __PYX_ERR(0, 659, __pyx_L1_error)); @@ -49341,9 +49525,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -49352,16 +49536,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -49370,8 +49554,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -49380,8 +49564,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -49400,12 +49584,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":701 * ssl[u] = l @@ -49414,8 +49598,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -49424,8 +49608,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -49434,8 +49618,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; 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- *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":708 * l = ssl[u] + 1 @@ -49497,8 +49681,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * else: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":709 * ssl[u] = l @@ -49527,8 +49711,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_194ssl01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; 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+ if (likely(__pyx_t_28)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); - __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -49808,7 +49992,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -49833,6 +50017,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_197ssl01_scan(PyObject __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_v_stat = 0; PyObject *__pyx_v_kwargs = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ssl01_scan (wrapper)", 0); @@ -49933,24 +50120,20 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; + int __pyx_t_24; + __pyx_t_5numpy_float64_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; - int __pyx_t_31; - __pyx_t_5numpy_float64_t __pyx_t_32; - Py_ssize_t __pyx_t_33; - Py_ssize_t __pyx_t_34; - PyObject *__pyx_t_35 = NULL; + PyObject *__pyx_t_28 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7ssl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_7ssl01_scan", __pyx_f[0], 659, 0, __PYX_ERR(0, 659, __pyx_L1_error)); @@ -50226,9 +50409,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -50237,16 +50420,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L15_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L15_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":698 * if a1 < 0 or a2 < 0: @@ -50255,8 +50438,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":699 * # missing allele, assume sharing continues @@ -50265,8 +50448,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":696 * for k in range(j+1, n_haplotypes): @@ -50285,12 +50468,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":701 * ssl[u] = l @@ -50299,8 +50482,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":702 * elif a1 == a2 == 0: @@ -50309,8 +50492,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":703 * l = ssl[u] + 1 @@ -50319,8 +50502,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * elif a1 == a2 == 1: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":704 * ssl[u] = l @@ -50348,12 +50531,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_196ssl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); 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- __Pyx_INCREF(__pyx_t_35); + __Pyx_INCREF(__pyx_t_28); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - __pyx_t_3 = (__pyx_t_35) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_35, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); - __Pyx_XDECREF(__pyx_t_35); __pyx_t_35 = 0; + __pyx_t_3 = (__pyx_t_28) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_28, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_28); __pyx_t_28 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 721, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -50693,7 +50876,7 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_5, 1, (PyObject *(*)(char *)) __p __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_35); + __Pyx_XDECREF(__pyx_t_28); __Pyx_AddTraceback("allel.opt.stats.ssl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -50728,6 +50911,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_29ihh01_scan(PyObject *__pyx_self, PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -50851,6 +51037,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_28ihh01_scan(CYTHON_UNUSED PyObject Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("ihh01_scan", 0); __Pyx_TraceCall("ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -51555,6 +51744,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_338__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_0ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -52115,9 +52306,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -52126,16 +52317,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -52144,8 +52335,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -52154,8 +52345,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -52174,12 +52365,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -52188,8 +52379,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -52198,8 +52389,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -52208,8 +52399,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -52227,8 +52418,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -52265,12 +52456,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -52279,8 +52470,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -52289,8 +52480,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -52299,8 +52490,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -52318,8 +52509,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -52357,8 +52548,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -52380,8 +52571,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -52443,8 +52634,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -52453,8 +52644,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_200ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; 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+ __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -52528,8 +52719,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -52541,13 +52732,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -52559,7 +52750,7 @@ __pyx_t_35.__pyx_n = 2; 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- __Pyx_XDECREF(__pyx_t_38); __pyx_t_38 = 0; + __pyx_t_3 = (__pyx_t_31) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_31, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_31); __pyx_t_31 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 818, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -52697,7 +52888,7 @@ __pyx_t_35.__pyx_n = 2; __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_38); + __Pyx_XDECREF(__pyx_t_31); __Pyx_AddTraceback("allel.opt.stats.ihh01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -52722,6 +52913,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_340__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_1ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -53282,9 +53475,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -53293,16 +53486,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -53311,8 +53504,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -53321,8 +53514,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -53341,12 +53534,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -53355,8 +53548,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -53365,8 +53558,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -53375,8 +53568,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -53394,8 +53587,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -53432,12 +53625,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -53446,8 +53639,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -53456,8 +53649,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -53466,8 +53659,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -53485,8 +53678,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -53524,8 +53717,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -53547,8 +53740,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -53610,8 +53803,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -53620,8 +53813,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_31 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_24 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_24 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":807 * # minor allele frequency below cutoff, don't bother to compute @@ -53630,8 +53823,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec * * else: */ - __pyx_t_32 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_32 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_25 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_25 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":804 * maf = c1 / (c0 + c1) @@ -53654,13 +53847,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec __pyx_t_5.data = __pyx_v_ssl00.data; __pyx_t_5.memview = __pyx_v_ssl00.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl00.shape[0], __pyx_v_ssl00.strides[0], __pyx_v_ssl00.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u00, 0, @@ -53672,7 +53865,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_202ihh01_scan(CYTHON_UNUSED PyObjec __PYX_ERR(0, 811, __pyx_L4_error) } -__pyx_t_35.__pyx_n = 2; +__pyx_t_28.__pyx_n = 2; /* "allel/opt/stats.pyx":813 * vstat0[i] = ssl2ihh(ssl00[:u00], l_max_00, i, gaps, @@ -53681,9 +53874,9 @@ __pyx_t_35.__pyx_n = 2; * vstat1[i] = ssl2ihh(ssl11[:u11], l_max_11, i, gaps, * min_ehh=min_ehh, */ - __pyx_t_35.min_ehh = __pyx_v_min_ehh; - __pyx_t_35.include_edges = __pyx_v_include_edges; - __pyx_t_34 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_35); + __pyx_t_28.min_ehh = __pyx_v_min_ehh; + __pyx_t_28.include_edges = __pyx_v_include_edges; + __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -53695,8 +53888,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -53708,13 +53901,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -53726,7 +53919,7 @@ __pyx_t_35.__pyx_n = 2; 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_2ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -54449,9 +54644,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -54460,16 +54655,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -54478,8 +54673,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -54488,8 +54683,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -54508,12 +54703,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -54522,8 +54717,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -54532,8 +54727,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -54542,8 +54737,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -54561,8 +54756,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -54599,12 +54794,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -54613,8 +54808,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -54623,8 +54818,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -54633,8 +54828,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -54652,8 +54847,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -54691,8 +54886,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -54714,8 +54909,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -54777,8 +54972,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -54787,8 +54982,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_31 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_24 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_24 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":807 * # minor allele frequency below cutoff, don't bother to compute @@ -54797,8 +54992,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec * * else: */ - __pyx_t_32 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_32 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_25 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_25 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":804 * maf = c1 / (c0 + c1) @@ -54821,13 +55016,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_204ihh01_scan(CYTHON_UNUSED PyObjec __pyx_t_5.data = __pyx_v_ssl00.data; 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+ __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -54862,8 +55057,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -54875,13 +55070,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -54893,7 +55088,7 @@ __pyx_t_35.__pyx_n = 2; 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- __Pyx_XDECREF(__pyx_t_38); __pyx_t_38 = 0; + __pyx_t_3 = (__pyx_t_31) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_31, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_31); __pyx_t_31 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 818, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -55031,7 +55226,7 @@ __pyx_t_35.__pyx_n = 2; __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_38); + __Pyx_XDECREF(__pyx_t_31); __Pyx_AddTraceback("allel.opt.stats.ihh01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -55056,6 +55251,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_344__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_3ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -55616,9 +55813,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -55627,16 +55824,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -55645,8 +55842,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -55655,8 +55852,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -55675,12 +55872,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -55689,8 +55886,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -55699,8 +55896,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -55709,8 +55906,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -55728,8 +55925,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -55766,12 +55963,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -55780,8 +55977,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -55790,8 +55987,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -55800,8 +55997,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -55819,8 +56016,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -55858,8 +56055,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -55881,8 +56078,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -55944,8 +56141,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -55954,8 +56151,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_206ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; 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+ __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -56029,8 +56226,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -56042,13 +56239,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -56060,7 +56257,7 @@ __pyx_t_35.__pyx_n = 2; 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- __Pyx_XDECREF(__pyx_t_38); __pyx_t_38 = 0; + __pyx_t_3 = (__pyx_t_31) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_31, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_31); __pyx_t_31 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 818, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -56198,7 +56395,7 @@ __pyx_t_35.__pyx_n = 2; __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_38); + __Pyx_XDECREF(__pyx_t_31); __Pyx_AddTraceback("allel.opt.stats.ihh01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -56223,6 +56420,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_346__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_4ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -56783,9 +56982,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -56794,16 +56993,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -56812,8 +57011,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -56822,8 +57021,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -56842,12 +57041,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -56856,8 +57055,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -56866,8 +57065,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -56876,8 +57075,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -56895,8 +57094,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -56933,12 +57132,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -56947,8 +57146,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -56957,8 +57156,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -56967,8 +57166,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -56986,8 +57185,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -57025,8 +57224,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -57048,8 +57247,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -57111,8 +57310,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -57121,8 +57320,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_208ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; 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+ __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -57196,8 +57395,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -57209,13 +57408,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -57227,7 +57426,7 @@ __pyx_t_35.__pyx_n = 2; 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_5ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -57950,9 +58151,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -57961,16 +58162,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -57979,8 +58180,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -57989,8 +58190,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -58009,12 +58210,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -58023,8 +58224,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -58033,8 +58234,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -58043,8 +58244,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -58062,8 +58263,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -58100,12 +58301,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -58114,8 +58315,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -58124,8 +58325,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -58134,8 +58335,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -58153,8 +58354,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -58192,8 +58393,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -58215,8 +58416,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -58278,8 +58479,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -58288,8 +58489,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_31 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_24 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_24 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":807 * # minor allele frequency below cutoff, don't bother to compute @@ -58298,8 +58499,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec * * else: */ - __pyx_t_32 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_32 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_25 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_25 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":804 * maf = c1 / (c0 + c1) @@ -58322,13 +58523,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec __pyx_t_5.data = __pyx_v_ssl00.data; __pyx_t_5.memview = __pyx_v_ssl00.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl00.shape[0], __pyx_v_ssl00.strides[0], __pyx_v_ssl00.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u00, 0, @@ -58340,7 +58541,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_210ihh01_scan(CYTHON_UNUSED PyObjec __PYX_ERR(0, 811, __pyx_L4_error) } -__pyx_t_35.__pyx_n = 2; +__pyx_t_28.__pyx_n = 2; /* "allel/opt/stats.pyx":813 * vstat0[i] = ssl2ihh(ssl00[:u00], l_max_00, i, gaps, @@ -58349,9 +58550,9 @@ __pyx_t_35.__pyx_n = 2; * vstat1[i] = ssl2ihh(ssl11[:u11], l_max_11, i, gaps, * min_ehh=min_ehh, */ - __pyx_t_35.min_ehh = __pyx_v_min_ehh; - __pyx_t_35.include_edges = __pyx_v_include_edges; - __pyx_t_34 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_35); + __pyx_t_28.min_ehh = __pyx_v_min_ehh; + __pyx_t_28.include_edges = __pyx_v_include_edges; + __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -58363,8 +58564,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -58376,13 +58577,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -58394,7 +58595,7 @@ __pyx_t_35.__pyx_n = 2; 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- Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_6ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -59117,9 +59320,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -59128,16 +59331,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -59146,8 +59349,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -59156,8 +59359,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -59176,12 +59379,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -59190,8 +59393,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -59200,8 +59403,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -59210,8 +59413,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -59229,8 +59432,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -59267,12 +59470,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -59281,8 +59484,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -59291,8 +59494,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -59301,8 +59504,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -59320,8 +59523,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -59359,8 +59562,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -59382,8 +59585,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -59445,8 +59648,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -59455,8 +59658,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_31 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_24 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_24 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":807 * # minor allele frequency below cutoff, don't bother to compute @@ -59465,8 +59668,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec * * else: */ - __pyx_t_32 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_32 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_25 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_25 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; /* "allel/opt/stats.pyx":804 * maf = c1 / (c0 + c1) @@ -59489,13 +59692,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_212ihh01_scan(CYTHON_UNUSED PyObjec __pyx_t_5.data = __pyx_v_ssl00.data; 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- __Pyx_XDECREF(__pyx_t_38); __pyx_t_38 = 0; + __pyx_t_3 = (__pyx_t_31) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_31, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_31); __pyx_t_31 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 818, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -59699,7 +59902,7 @@ __pyx_t_35.__pyx_n = 2; __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_38); + __Pyx_XDECREF(__pyx_t_31); __Pyx_AddTraceback("allel.opt.stats.ihh01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -59724,6 +59927,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_352__defaults__(CYTHON_UNUSED PyObj PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__defaults__", 0); __Pyx_TraceCall("__defaults__", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); __Pyx_XDECREF(__pyx_r); @@ -59780,6 +59986,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_215ihh01_scan(PyObject __pyx_t_5numpy_float64_t __pyx_v_min_ehh; __pyx_t_5numpy_float64_t __pyx_v_min_maf; int __pyx_v_include_edges; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ihh01_scan (wrapper)", 0); @@ -59927,27 +60136,23 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; Py_ssize_t __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; + int __pyx_t_26; + __pyx_t_5numpy_float64_t __pyx_t_27; + struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; - Py_ssize_t __pyx_t_31; - Py_ssize_t __pyx_t_32; - int __pyx_t_33; - __pyx_t_5numpy_float64_t __pyx_t_34; - struct __pyx_opt_args_5allel_3opt_5stats_ssl2ihh __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_31 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7ihh01_scan", 0); __Pyx_TraceCall("__pyx_fuse_7ihh01_scan", __pyx_f[0], 726, 0, __PYX_ERR(0, 726, __pyx_L1_error)); @@ -60284,9 +60489,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -60295,16 +60500,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":777 * if a1 < 0 or a2 < 0: @@ -60313,8 +60518,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * elif a1 == a2 == 0: */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":778 * # missing allele, assume sharing continues @@ -60323,8 +60528,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_23 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":775 * for k in range(j+1, n_haplotypes): @@ -60343,12 +60548,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":780 * ssl[u] = l @@ -60357,8 +60562,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl00[u00] = l */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_14 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":781 * elif a1 == a2 == 0: @@ -60367,8 +60572,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * ssl00[u00] = l * u00 += 1 */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_14 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_14 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":782 * l = ssl[u] + 1 @@ -60377,8 +60582,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * u00 += 1 * if l > l_max_00: */ - __pyx_t_26 = __pyx_v_u00; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_26 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; + __pyx_t_20 = __pyx_v_u00; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl00.data + __pyx_t_20 * __pyx_v_ssl00.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":783 * ssl[u] = l @@ -60396,8 +60601,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * l_max_00 = l * elif a1 == a2 == 1: */ - __pyx_t_21 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); - if (__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_l > __pyx_v_l_max_00) != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":785 * u00 += 1 @@ -60434,12 +60639,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl[u] = l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":787 * l_max_00 = l @@ -60448,8 +60653,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * ssl[u] = l * ssl11[u11] = l */ - __pyx_t_27 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_27 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_21 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":788 * elif a1 == a2 == 1: @@ -60458,8 +60663,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * ssl11[u11] = l * u11 += 1 */ - __pyx_t_28 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_28 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_21 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_21 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":789 * l = ssl[u] + 1 @@ -60468,8 +60673,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * u11 += 1 * if l > l_max_11: */ - __pyx_t_29 = __pyx_v_u11; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_29 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; + __pyx_t_22 = __pyx_v_u11; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl11.data + __pyx_t_22 * __pyx_v_ssl11.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":790 * ssl[u] = l @@ -60487,8 +60692,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * l_max_11 = l * else: */ - __pyx_t_20 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_l > __pyx_v_l_max_11) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":792 * u11 += 1 @@ -60526,8 +60731,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * */ /*else*/ { - __pyx_t_30 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_30 * __pyx_v_ssl.strides[0]) )) = 0; + __pyx_t_23 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) )) = 0; } __pyx_L12:; @@ -60549,8 +60754,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * maf = c0 / (c0 + c1) * else: */ - __pyx_t_20 = ((__pyx_v_c0 < __pyx_v_c1) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_c0 < __pyx_v_c1) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":800 * # compute minor allele frequency @@ -60612,8 +60817,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * # minor allele frequency below cutoff, don't bother to compute * vstat0[i] = nan64 */ - __pyx_t_20 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_maf < __pyx_v_min_maf) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":806 * if maf < min_maf: @@ -60622,8 +60827,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_214ihh01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = nan64 * */ - __pyx_t_31 = __pyx_v_i; 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+ __pyx_t_27 = __pyx_f_5allel_3opt_5stats_ssl2ihh(__pyx_t_5, __pyx_v_l_max_00, __pyx_v_i, __pyx_v_gaps, 0, &__pyx_t_28); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 0); __pyx_t_5.memview = NULL; __pyx_t_5.data = NULL; @@ -60697,8 +60902,8 @@ __pyx_t_35.__pyx_n = 2; * min_ehh=min_ehh, * include_edges=include_edges) */ - __pyx_t_36 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_36 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_34; + __pyx_t_29 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_29 * __pyx_v_vstat0.strides[0]) )) = __pyx_t_27; /* "allel/opt/stats.pyx":814 * min_ehh=min_ehh, @@ -60710,13 +60915,13 @@ __pyx_t_35.__pyx_n = 2; __pyx_t_5.data = __pyx_v_ssl11.data; __pyx_t_5.memview = __pyx_v_ssl11.memview; __PYX_INC_MEMVIEW(&__pyx_t_5, 0); - __pyx_t_33 = -1; + __pyx_t_26 = -1; if (unlikely(__pyx_memoryview_slice_memviewslice( &__pyx_t_5, __pyx_v_ssl11.shape[0], __pyx_v_ssl11.strides[0], __pyx_v_ssl11.suboffsets[0], 0, 0, - &__pyx_t_33, + &__pyx_t_26, 0, __pyx_v_u11, 0, @@ -60728,7 +60933,7 @@ __pyx_t_35.__pyx_n = 2; 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- __Pyx_XDECREF(__pyx_t_38); __pyx_t_38 = 0; + __pyx_t_3 = (__pyx_t_31) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_31, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_4); + __Pyx_XDECREF(__pyx_t_31); __pyx_t_31 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 818, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -60866,7 +61071,7 @@ __pyx_t_35.__pyx_n = 2; __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_38); + __Pyx_XDECREF(__pyx_t_31); __Pyx_AddTraceback("allel.opt.stats.ihh01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -60900,6 +61105,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_31nsl01_scan(PyObject *__pyx_self, PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); 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PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl01_scan (wrapper)", 0); @@ -61779,19 +61993,15 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - PyObject *__pyx_t_30 = NULL; + PyObject *__pyx_t_23 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0nsl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_0nsl01_scan", __pyx_f[0], 823, 0, __PYX_ERR(0, 823, __pyx_L1_error)); @@ -62011,9 +62221,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; 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__pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":863 * if a1 < 0 or a2 < 0: @@ -62040,8 +62250,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -62060,12 +62270,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl00_sum += l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":865 * l = ssl[u] + 1 @@ -62074,8 +62284,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * ssl00_sum += l * u00 += 1 */ - __pyx_t_23 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":866 * elif a1 == a2 == 0: @@ -62112,12 +62322,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl11_sum += l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -62126,8 +62336,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -62176,8 +62386,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":876 * l = 0 @@ -62197,8 +62407,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * vstat0[i] = ssl00_sum / u00 * else: */ - __pyx_t_20 = ((__pyx_v_u00 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u00 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":879 * @@ -62217,8 +62427,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 879, __pyx_L4_error) } - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_26 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_14 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); /* "allel/opt/stats.pyx":878 * u += 1 @@ -62238,8 +62448,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 */ /*else*/ { - __pyx_t_27 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_27 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_20 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_20 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L15:; @@ -62250,8 +62460,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 * else: */ - __pyx_t_20 = ((__pyx_v_u11 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u11 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":883 * vstat0[i] = nan64 @@ -62270,8 +62480,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 883, __pyx_L4_error) } - __pyx_t_28 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_28 * __pyx_v_vstat1.strides[0]) )) = (((double)__pyx_v_ssl11_sum) / ((double)__pyx_v_u11)); + __pyx_t_21 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_21 * __pyx_v_vstat1.strides[0]) )) = (((double)__pyx_v_ssl11_sum) / ((double)__pyx_v_u11)); /* "allel/opt/stats.pyx":882 * else: @@ -62291,8 +62501,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec * return np.asarray(vstat0), np.asarray(vstat1) */ /*else*/ { - __pyx_t_29 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_29 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_22 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_22 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L16:; } @@ -62362,18 +62572,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_vstat1, 1, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_5numpy_float64_t, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_5numpy_float64_t, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_30 = NULL; + __pyx_t_23 = NULL; if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_30 = PyMethod_GET_SELF(__pyx_t_4); - if (likely(__pyx_t_30)) { + __pyx_t_23 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_23)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); - __Pyx_INCREF(__pyx_t_30); + __Pyx_INCREF(__pyx_t_23); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_4, function); } } - __pyx_t_3 = (__pyx_t_30) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_30, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); - __Pyx_XDECREF(__pyx_t_30); __pyx_t_30 = 0; + __pyx_t_3 = (__pyx_t_23) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_23, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); + __Pyx_XDECREF(__pyx_t_23); __pyx_t_23 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -62406,7 +62616,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_218nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_30); + __Pyx_XDECREF(__pyx_t_23); __Pyx_AddTraceback("allel.opt.stats.nsl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -62425,6 +62635,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_221nsl01_scan(PyObject static PyMethodDef __pyx_fuse_1__pyx_mdef_5allel_3opt_5stats_221nsl01_scan = {"__pyx_fuse_1nsl01_scan", (PyCFunction)__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_221nsl01_scan, METH_O, __pyx_doc_5allel_3opt_5stats_30nsl01_scan}; static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_221nsl01_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl01_scan (wrapper)", 0); @@ -62482,19 +62695,15 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - PyObject *__pyx_t_30 = NULL; + PyObject *__pyx_t_23 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1nsl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_1nsl01_scan", __pyx_f[0], 823, 0, __PYX_ERR(0, 823, __pyx_L1_error)); @@ -62714,9 +62923,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -62725,16 +62934,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":863 * if a1 < 0 or a2 < 0: @@ -62743,8 +62952,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -62763,12 +62972,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl00_sum += l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":865 * l = ssl[u] + 1 @@ -62777,8 +62986,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * ssl00_sum += l * u00 += 1 */ - __pyx_t_23 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":866 * elif a1 == a2 == 0: @@ -62815,12 +63024,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl11_sum += l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -62829,8 +63038,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -62879,8 +63088,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":876 * l = 0 @@ -62900,8 +63109,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * vstat0[i] = ssl00_sum / u00 * else: */ - __pyx_t_20 = ((__pyx_v_u00 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u00 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":879 * @@ -62920,8 +63129,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 879, __pyx_L4_error) } - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_26 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_14 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); /* "allel/opt/stats.pyx":878 * u += 1 @@ -62941,8 +63150,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 */ /*else*/ { - __pyx_t_27 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_27 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_20 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_20 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L15:; @@ -62953,8 +63162,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 * else: */ - __pyx_t_20 = ((__pyx_v_u11 > 0) != 0); 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__Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_4, function); } } - __pyx_t_3 = (__pyx_t_30) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_30, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); - __Pyx_XDECREF(__pyx_t_30); __pyx_t_30 = 0; + __pyx_t_3 = (__pyx_t_23) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_23, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); + __Pyx_XDECREF(__pyx_t_23); __pyx_t_23 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -63109,7 +63318,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_220nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_30); + __Pyx_XDECREF(__pyx_t_23); __Pyx_AddTraceback("allel.opt.stats.nsl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -63128,6 +63337,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_223nsl01_scan(PyObject static PyMethodDef __pyx_fuse_2__pyx_mdef_5allel_3opt_5stats_223nsl01_scan = {"__pyx_fuse_2nsl01_scan", (PyCFunction)__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_223nsl01_scan, METH_O, __pyx_doc_5allel_3opt_5stats_30nsl01_scan}; 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+ const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2nsl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_2nsl01_scan", __pyx_f[0], 823, 0, __PYX_ERR(0, 823, __pyx_L1_error)); @@ -63417,9 +63625,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -63428,16 +63636,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); 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+ __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -63532,8 +63740,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -63582,8 +63790,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":876 * l = 0 @@ -63603,8 +63811,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * vstat0[i] = ssl00_sum / u00 * else: */ - __pyx_t_20 = ((__pyx_v_u00 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u00 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":879 * @@ -63623,8 +63831,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 879, __pyx_L4_error) } - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_26 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_14 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); /* "allel/opt/stats.pyx":878 * u += 1 @@ -63644,8 +63852,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 */ /*else*/ { - __pyx_t_27 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_27 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_20 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_20 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L15:; @@ -63656,8 +63864,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 * else: */ - __pyx_t_20 = ((__pyx_v_u11 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u11 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":883 * vstat0[i] = nan64 @@ -63676,8 +63884,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_222nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 883, __pyx_L4_error) } - __pyx_t_28 = __pyx_v_i; 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+ __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":863 * if a1 < 0 or a2 < 0: @@ -64852,8 +65058,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_226nsl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -64872,12 +65078,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_226nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl00_sum += l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); 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+ __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -64938,8 +65144,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_226nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -64988,8 +65194,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_226nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; 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+ __Pyx_XDECREF(__pyx_t_23); __pyx_t_23 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -65218,7 +65424,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_226nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_30); + __Pyx_XDECREF(__pyx_t_23); __Pyx_AddTraceback("allel.opt.stats.nsl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -65237,6 +65443,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_229nsl01_scan(PyObject static PyMethodDef __pyx_fuse_5__pyx_mdef_5allel_3opt_5stats_229nsl01_scan = {"__pyx_fuse_5nsl01_scan", (PyCFunction)__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_229nsl01_scan, METH_O, __pyx_doc_5allel_3opt_5stats_30nsl01_scan}; static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_229nsl01_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; 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@@ -65526,9 +65731,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -65537,16 +65742,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":863 * if a1 < 0 or a2 < 0: @@ -65555,8 +65760,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -65575,12 +65780,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl00_sum += l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":865 * l = ssl[u] + 1 @@ -65589,8 +65794,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * ssl00_sum += l * u00 += 1 */ - __pyx_t_23 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":866 * elif a1 == a2 == 0: @@ -65627,12 +65832,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl11_sum += l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -65641,8 +65846,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -65691,8 +65896,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; 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/* "allel/opt/stats.pyx":878 * u += 1 @@ -65753,8 +65958,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 */ /*else*/ { - __pyx_t_27 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_27 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_20 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_20 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L15:; @@ -65765,8 +65970,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 * else: */ - __pyx_t_20 = ((__pyx_v_u11 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u11 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":883 * vstat0[i] = nan64 @@ -65785,8 +65990,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 883, __pyx_L4_error) } - __pyx_t_28 = __pyx_v_i; 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__pyx_t_2 = 0; __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_vstat1, 1, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_5numpy_float64_t, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_5numpy_float64_t, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_30 = NULL; + __pyx_t_23 = NULL; if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_30 = PyMethod_GET_SELF(__pyx_t_4); - if (likely(__pyx_t_30)) { + __pyx_t_23 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_23)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); - __Pyx_INCREF(__pyx_t_30); + __Pyx_INCREF(__pyx_t_23); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_4, function); } } - __pyx_t_3 = (__pyx_t_30) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_30, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); - __Pyx_XDECREF(__pyx_t_30); __pyx_t_30 = 0; + __pyx_t_3 = (__pyx_t_23) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_23, __pyx_t_2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); + __Pyx_XDECREF(__pyx_t_23); __pyx_t_23 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 887, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); @@ -65921,7 +66126,7 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_228nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_XDECREF(__pyx_t_4); __PYX_XDEC_MEMVIEW(&__pyx_t_5, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_6, 1); - __Pyx_XDECREF(__pyx_t_30); + __Pyx_XDECREF(__pyx_t_23); __Pyx_AddTraceback("allel.opt.stats.nsl01_scan", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -65940,6 +66145,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_231nsl01_scan(PyObject static PyMethodDef __pyx_fuse_6__pyx_mdef_5allel_3opt_5stats_231nsl01_scan = {"__pyx_fuse_6nsl01_scan", (PyCFunction)__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_231nsl01_scan, METH_O, __pyx_doc_5allel_3opt_5stats_30nsl01_scan}; static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_231nsl01_scan(PyObject *__pyx_self, PyObject *__pyx_arg_h) { __Pyx_memviewslice __pyx_v_h = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("nsl01_scan (wrapper)", 0); @@ -65997,19 +66205,15 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; + int __pyx_t_18; + int __pyx_t_19; + Py_ssize_t __pyx_t_20; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; - Py_ssize_t __pyx_t_23; - Py_ssize_t __pyx_t_24; - Py_ssize_t __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - PyObject *__pyx_t_30 = NULL; + PyObject *__pyx_t_23 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6nsl01_scan", 0); __Pyx_TraceCall("__pyx_fuse_6nsl01_scan", __pyx_f[0], 823, 0, __PYX_ERR(0, 823, __pyx_L1_error)); @@ -66229,9 +66433,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -66240,16 +66444,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; + __pyx_t_18 = __pyx_t_19; goto __pyx_L13_bool_binop_done; } - __pyx_t_21 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_20 = __pyx_t_21; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_18 = __pyx_t_19; __pyx_L13_bool_binop_done:; - if (__pyx_t_20) { + if (__pyx_t_18) { /* "allel/opt/stats.pyx":863 * if a1 < 0 or a2 < 0: @@ -66258,8 +66462,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * elif a1 == a2 == 0: * l = ssl[u] + 1 */ - __pyx_t_22 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_22 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -66278,12 +66482,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl00_sum += l */ - __pyx_t_20 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":865 * l = ssl[u] + 1 @@ -66292,8 +66496,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * ssl00_sum += l * u00 += 1 */ - __pyx_t_23 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":866 * elif a1 == a2 == 0: @@ -66330,12 +66534,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl11_sum += l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); + __pyx_t_19 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_19) { + __pyx_t_19 = (__pyx_v_a2 == 1); } - __pyx_t_20 = (__pyx_t_21 != 0); - if (__pyx_t_20) { + __pyx_t_18 = (__pyx_t_19 != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":869 * u00 += 1 @@ -66344,8 +66548,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * ssl11_sum += l * u11 += 1 */ - __pyx_t_24 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_24 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":870 * elif a1 == a2 == 1: @@ -66394,8 +66598,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * u += 1 * */ - __pyx_t_25 = __pyx_v_u; - *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_25 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; + __pyx_t_13 = __pyx_v_u; + *((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) )) = __pyx_v_l; /* "allel/opt/stats.pyx":876 * l = 0 @@ -66415,8 +66619,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * vstat0[i] = ssl00_sum / u00 * else: */ - __pyx_t_20 = ((__pyx_v_u00 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u00 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":879 * @@ -66435,8 +66639,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 879, __pyx_L4_error) } - __pyx_t_26 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_26 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); + __pyx_t_14 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_14 * __pyx_v_vstat0.strides[0]) )) = (((double)__pyx_v_ssl00_sum) / ((double)__pyx_v_u00)); /* "allel/opt/stats.pyx":878 * u += 1 @@ -66456,8 +66660,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 */ /*else*/ { - __pyx_t_27 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_27 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_20 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat0.data + __pyx_t_20 * __pyx_v_vstat0.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L15:; @@ -66468,8 +66672,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * vstat1[i] = ssl11_sum / u11 * else: */ - __pyx_t_20 = ((__pyx_v_u11 > 0) != 0); - if (__pyx_t_20) { + __pyx_t_18 = ((__pyx_v_u11 > 0) != 0); + if (__pyx_t_18) { /* "allel/opt/stats.pyx":883 * vstat0[i] = nan64 @@ -66488,8 +66692,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec #endif __PYX_ERR(0, 883, __pyx_L4_error) } - __pyx_t_28 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_28 * __pyx_v_vstat1.strides[0]) )) = (((double)__pyx_v_ssl11_sum) / ((double)__pyx_v_u11)); + __pyx_t_21 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_21 * __pyx_v_vstat1.strides[0]) )) = (((double)__pyx_v_ssl11_sum) / ((double)__pyx_v_u11)); /* "allel/opt/stats.pyx":882 * else: @@ -66509,8 +66713,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec * return np.asarray(vstat0), np.asarray(vstat1) */ /*else*/ { - __pyx_t_29 = __pyx_v_i; - *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_29 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; + __pyx_t_22 = __pyx_v_i; + *((__pyx_t_5numpy_float64_t *) ( /* dim=0 */ (__pyx_v_vstat1.data + __pyx_t_22 * __pyx_v_vstat1.strides[0]) )) = __pyx_v_5allel_3opt_5stats_nan64; } __pyx_L16:; } @@ -66580,18 +66784,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_230nsl01_scan(CYTHON_UNUSED PyObjec __Pyx_DECREF(__pyx_t_2); 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@@ -66932,9 +67135,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_232nsl01_scan(CYTHON_UNUSED PyObjec * if a1 < 0 or a2 < 0: * # missing allele, assume sharing continues */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = __pyx_v_k; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_18 * __pyx_v_h.strides[0]) ) + __pyx_t_19 * __pyx_v_h.strides[1]) ))); + __pyx_t_14 = __pyx_v_i; + __pyx_t_13 = __pyx_v_k; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_h.data + __pyx_t_14 * __pyx_v_h.strides[0]) ) + __pyx_t_13 * __pyx_v_h.strides[1]) ))); /* "allel/opt/stats.pyx":861 * for k in range(j+1, n_haplotypes): @@ -66943,16 +67146,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_232nsl01_scan(CYTHON_UNUSED PyObjec * # missing allele, assume sharing continues * l = ssl[u] + 1 */ - __pyx_t_21 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_21) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_20 = __pyx_t_21; 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- if (__pyx_t_20) { - __pyx_t_20 = (__pyx_v_a2 == 0); + __pyx_t_18 = (__pyx_v_a1 == __pyx_v_a2); + if (__pyx_t_18) { + __pyx_t_18 = (__pyx_v_a2 == 0); } - __pyx_t_21 = (__pyx_t_20 != 0); - if (__pyx_t_21) { + __pyx_t_19 = (__pyx_t_18 != 0); + if (__pyx_t_19) { /* "allel/opt/stats.pyx":865 * l = ssl[u] + 1 @@ -66995,8 +67198,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_232nsl01_scan(CYTHON_UNUSED PyObjec * ssl00_sum += l * u00 += 1 */ - __pyx_t_23 = __pyx_v_u; - __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_23 * __pyx_v_ssl.strides[0]) ))) + 1); + __pyx_t_13 = __pyx_v_u; + __pyx_v_l = ((*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_ssl.data + __pyx_t_13 * __pyx_v_ssl.strides[0]) ))) + 1); /* "allel/opt/stats.pyx":866 * elif a1 == a2 == 0: @@ -67033,12 +67236,12 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_232nsl01_scan(CYTHON_UNUSED PyObjec * l = ssl[u] + 1 * ssl11_sum += l */ - __pyx_t_21 = (__pyx_v_a1 == __pyx_v_a2); - if (__pyx_t_21) { - __pyx_t_21 = (__pyx_v_a2 == 1); 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Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("phase_progeny_by_transmission", 0); __Pyx_TraceCall("phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -68179,6 +68388,9 @@ static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_237phase_progeny_by_tra static PyMethodDef __pyx_fuse_0__pyx_mdef_5allel_3opt_5stats_237phase_progeny_by_transmission = {"__pyx_fuse_0phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_237phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_237phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -68229,8 +68441,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; + int __pyx_t_13; + int __pyx_t_14; Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; @@ -68238,8 +68450,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; + Py_ssize_t __pyx_t_22; + Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; @@ -68257,38 +68469,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_0phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -68509,10 +68692,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -68521,10 +68704,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -68533,10 +68716,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -68545,28 +68728,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -68637,8 +68820,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_10 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_10 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -68647,8 +68830,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_11 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_11 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -68657,8 +68840,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_12 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_12 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -68667,8 +68850,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_15 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -68677,10 +68860,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_16 = (__pyx_v_n_progeny + 2); + __pyx_t_17 = __pyx_t_16; + for (__pyx_t_18 = 2; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { + __pyx_v_j = __pyx_t_18; /* "allel/opt/stats.pyx":941 * @@ -68689,10 +68872,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_21 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -68701,10 +68884,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_19 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -68713,16 +68896,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -68749,8 +68932,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -68759,18 +68942,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_19 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_19 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -68779,9 +68962,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_19 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -68810,25 +68993,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_21 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_21 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -68837,9 +69020,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_22 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_22 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -68858,25 +69041,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_23 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_23 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -68885,10 +69068,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_23 = __pyx_v_i; + __pyx_t_24 = __pyx_v_j; + __pyx_t_25 = 0; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_23 * __pyx_v_g.strides[0]) ) + __pyx_t_24 * __pyx_v_g.strides[1]) ) + __pyx_t_25 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -68897,10 +69080,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_j; + __pyx_t_28 = 1; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_26 * __pyx_v_g.strides[0]) ) + __pyx_t_27 * __pyx_v_g.strides[1]) ) + __pyx_t_28 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -68909,9 +69092,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_29 = __pyx_v_i; + __pyx_t_30 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_29 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_30 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -68930,25 +69113,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_31 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_31 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -68957,10 +69140,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_31 = __pyx_v_i; + __pyx_t_32 = __pyx_v_j; + __pyx_t_33 = 0; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -68969,10 +69152,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_j; + __pyx_t_36 = 1; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -68981,9 +69164,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_37 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_38 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -69002,25 +69185,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_39 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_39 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -69029,9 +69212,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_236phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_39 = __pyx_v_i; + __pyx_t_40 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -69097,6 +69280,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_239phase_progeny_by_tra static PyMethodDef __pyx_fuse_1__pyx_mdef_5allel_3opt_5stats_239phase_progeny_by_transmission = {"__pyx_fuse_1phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_239phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_239phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -69147,8 +69333,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; + int __pyx_t_13; + int __pyx_t_14; Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; @@ -69156,8 +69342,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; + Py_ssize_t __pyx_t_22; + Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; @@ -69175,38 +69361,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_1phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -69427,10 +69584,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -69439,10 +69596,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -69451,10 +69608,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -69463,28 +69620,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -69555,8 +69712,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_10 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_10 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -69565,8 +69722,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_11 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_11 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -69575,8 +69732,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_12 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_12 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -69585,8 +69742,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_15 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -69595,10 +69752,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_16 = (__pyx_v_n_progeny + 2); + __pyx_t_17 = __pyx_t_16; + for (__pyx_t_18 = 2; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { + __pyx_v_j = __pyx_t_18; /* "allel/opt/stats.pyx":941 * @@ -69607,10 +69764,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_21 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -69619,10 +69776,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_19 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -69631,16 +69788,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -69667,8 +69824,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -69677,18 +69834,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_19 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_19 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -69697,9 +69854,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_19 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -69728,25 +69885,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_21 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_21 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -69755,9 +69912,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_22 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_22 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -69776,25 +69933,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_23 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_23 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -69803,10 +69960,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_23 = __pyx_v_i; + __pyx_t_24 = __pyx_v_j; + __pyx_t_25 = 0; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_23 * __pyx_v_g.strides[0]) ) + __pyx_t_24 * __pyx_v_g.strides[1]) ) + __pyx_t_25 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -69815,10 +69972,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_j; + __pyx_t_28 = 1; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_26 * __pyx_v_g.strides[0]) ) + __pyx_t_27 * __pyx_v_g.strides[1]) ) + __pyx_t_28 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -69827,9 +69984,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_29 = __pyx_v_i; + __pyx_t_30 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_29 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_30 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -69848,25 +70005,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_31 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_31 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -69875,10 +70032,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_31 = __pyx_v_i; + __pyx_t_32 = __pyx_v_j; + __pyx_t_33 = 0; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -69887,10 +70044,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_j; + __pyx_t_36 = 1; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -69899,9 +70056,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_37 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_38 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -69920,25 +70077,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_39 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_39 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -69947,9 +70104,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_238phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_39 = __pyx_v_i; + __pyx_t_40 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -70015,6 +70172,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_241phase_progeny_by_tra static PyMethodDef __pyx_fuse_2__pyx_mdef_5allel_3opt_5stats_241phase_progeny_by_transmission = {"__pyx_fuse_2phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_241phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_241phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -70065,8 +70225,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; + int __pyx_t_13; + int __pyx_t_14; Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; @@ -70074,8 +70234,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; + Py_ssize_t __pyx_t_22; + Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; @@ -70093,38 +70253,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_2phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -70345,10 +70476,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -70357,10 +70488,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -70369,10 +70500,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -70381,28 +70512,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -70473,8 +70604,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_10 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_10 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -70483,8 +70614,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_11 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_11 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -70493,8 +70624,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_12 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_12 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -70503,8 +70634,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_15 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -70513,10 +70644,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_16 = (__pyx_v_n_progeny + 2); + __pyx_t_17 = __pyx_t_16; + for (__pyx_t_18 = 2; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { + __pyx_v_j = __pyx_t_18; /* "allel/opt/stats.pyx":941 * @@ -70525,10 +70656,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_21 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -70537,10 +70668,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_19 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -70549,16 +70680,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -70585,8 +70716,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -70595,18 +70726,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_19 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_19 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_19 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -70615,9 +70746,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_19 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -70646,25 +70777,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_21 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_21 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_21 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_21 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -70673,9 +70804,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_22 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_22 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -70694,25 +70825,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_23 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_23 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_23 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_23 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -70721,10 +70852,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_23 = __pyx_v_i; + __pyx_t_24 = __pyx_v_j; + __pyx_t_25 = 0; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_23 * __pyx_v_g.strides[0]) ) + __pyx_t_24 * __pyx_v_g.strides[1]) ) + __pyx_t_25 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -70733,10 +70864,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_j; + __pyx_t_28 = 1; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_26 * __pyx_v_g.strides[0]) ) + __pyx_t_27 * __pyx_v_g.strides[1]) ) + __pyx_t_28 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -70745,9 +70876,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_29 = __pyx_v_i; + __pyx_t_30 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_29 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_30 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -70766,25 +70897,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_31 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_31 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_31 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_31 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -70793,10 +70924,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_31 = __pyx_v_i; + __pyx_t_32 = __pyx_v_j; + __pyx_t_33 = 0; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -70805,10 +70936,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_j; + __pyx_t_36 = 1; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -70817,9 +70948,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_37 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_38 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -70838,25 +70969,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_39 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_39 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_39 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_39 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -70865,9 +70996,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_240phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_39 = __pyx_v_i; + __pyx_t_40 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -70933,6 +71064,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_243phase_progeny_by_tra static PyMethodDef __pyx_fuse_3__pyx_mdef_5allel_3opt_5stats_243phase_progeny_by_transmission = {"__pyx_fuse_3phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_243phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_243phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -70983,21 +71117,21 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + int __pyx_t_13; + int __pyx_t_14; + __pyx_t_5numpy_int64_t __pyx_t_15; + __pyx_t_5numpy_int64_t __pyx_t_16; + __pyx_t_5numpy_int64_t __pyx_t_17; + __pyx_t_5numpy_int64_t __pyx_t_18; Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - __pyx_t_5numpy_int64_t __pyx_t_24; - __pyx_t_5numpy_int64_t __pyx_t_25; - __pyx_t_5numpy_int64_t __pyx_t_26; - __pyx_t_5numpy_int64_t __pyx_t_27; + __pyx_t_5numpy_int64_t __pyx_t_22; + Py_ssize_t __pyx_t_23; + Py_ssize_t __pyx_t_24; + Py_ssize_t __pyx_t_25; + Py_ssize_t __pyx_t_26; + Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; @@ -71007,42 +71141,14 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; Py_ssize_t __pyx_t_36; - __pyx_t_5numpy_int64_t __pyx_t_37; - __pyx_t_5numpy_int64_t __pyx_t_38; + Py_ssize_t __pyx_t_37; + Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - __pyx_t_5numpy_int64_t __pyx_t_41; - __pyx_t_5numpy_int64_t __pyx_t_42; - __pyx_t_5numpy_int64_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - __pyx_t_5numpy_int64_t __pyx_t_46; - __pyx_t_5numpy_int64_t __pyx_t_47; - __pyx_t_5numpy_int64_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - __pyx_t_5numpy_int64_t __pyx_t_57; - __pyx_t_5numpy_int64_t __pyx_t_58; - __pyx_t_5numpy_int64_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - __pyx_t_5numpy_int64_t __pyx_t_68; - __pyx_t_5numpy_int64_t __pyx_t_69; - __pyx_t_5numpy_int64_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + Py_ssize_t __pyx_t_41; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_3phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -71263,10 +71369,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -71275,10 +71381,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -71287,10 +71393,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -71299,28 +71405,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -71391,8 +71497,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_15 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -71401,8 +71507,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_16 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_16 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -71411,8 +71517,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_17 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_17 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -71421,8 +71527,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_18 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_18 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -71431,10 +71537,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_19 = (__pyx_v_n_progeny + 2); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 2; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_j = __pyx_t_21; /* "allel/opt/stats.pyx":941 * @@ -71443,10 +71549,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_12 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -71455,10 +71561,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_10 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -71467,16 +71573,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -71503,8 +71609,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -71513,18 +71619,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -71533,9 +71639,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_10 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_11 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -71564,25 +71670,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -71591,9 +71697,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_23 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_12 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_23 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -71612,25 +71718,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -71639,10 +71745,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_24 = __pyx_v_i; + __pyx_t_25 = __pyx_v_j; + __pyx_t_26 = 0; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_24 * __pyx_v_g.strides[0]) ) + __pyx_t_25 * __pyx_v_g.strides[1]) ) + __pyx_t_26 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -71651,10 +71757,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_27 = __pyx_v_i; + __pyx_t_28 = __pyx_v_j; + __pyx_t_29 = 1; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_27 * __pyx_v_g.strides[0]) ) + __pyx_t_28 * __pyx_v_g.strides[1]) ) + __pyx_t_29 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -71663,9 +71769,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_30 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -71684,25 +71790,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -71711,10 +71817,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_j; + __pyx_t_34 = 0; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -71723,10 +71829,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_35 = __pyx_v_i; + __pyx_t_36 = __pyx_v_j; + __pyx_t_37 = 1; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_35 * __pyx_v_g.strides[0]) ) + __pyx_t_36 * __pyx_v_g.strides[1]) ) + __pyx_t_37 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -71735,9 +71841,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_38 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_39 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -71756,25 +71862,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -71783,9 +71889,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_242phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_40 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_41 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -71851,6 +71957,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_245phase_progeny_by_tra static PyMethodDef __pyx_fuse_4__pyx_mdef_5allel_3opt_5stats_245phase_progeny_by_transmission = {"__pyx_fuse_4phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_245phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_245phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -71901,21 +72010,21 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + int __pyx_t_13; + int __pyx_t_14; + size_t __pyx_t_15; + size_t __pyx_t_16; + size_t __pyx_t_17; + size_t __pyx_t_18; Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - size_t __pyx_t_24; - size_t __pyx_t_25; - size_t __pyx_t_26; - size_t __pyx_t_27; + size_t __pyx_t_22; + Py_ssize_t __pyx_t_23; + Py_ssize_t __pyx_t_24; + Py_ssize_t __pyx_t_25; + Py_ssize_t __pyx_t_26; + Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; @@ -71925,42 +72034,14 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; Py_ssize_t __pyx_t_36; - size_t __pyx_t_37; - size_t __pyx_t_38; + Py_ssize_t __pyx_t_37; + Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - size_t __pyx_t_41; - size_t __pyx_t_42; - size_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - size_t __pyx_t_46; - size_t __pyx_t_47; - size_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - size_t __pyx_t_68; - size_t __pyx_t_69; - size_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + Py_ssize_t __pyx_t_41; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_4phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -72181,10 +72262,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -72193,10 +72274,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -72205,10 +72286,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -72217,28 +72298,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -72309,8 +72390,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_15 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -72319,8 +72400,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_16 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_16 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -72329,8 +72410,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_17 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_17 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -72339,8 +72420,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_18 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_18 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -72349,10 +72430,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_19 = (__pyx_v_n_progeny + 2); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 2; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_j = __pyx_t_21; /* "allel/opt/stats.pyx":941 * @@ -72361,10 +72442,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_12 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -72373,10 +72454,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_10 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -72385,16 +72466,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -72421,8 +72502,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -72431,18 +72512,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -72451,9 +72532,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_10 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_11 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -72482,25 +72563,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -72509,9 +72590,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_23 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_12 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_23 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -72530,25 +72611,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -72557,10 +72638,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_24 = __pyx_v_i; + __pyx_t_25 = __pyx_v_j; + __pyx_t_26 = 0; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_24 * __pyx_v_g.strides[0]) ) + __pyx_t_25 * __pyx_v_g.strides[1]) ) + __pyx_t_26 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -72569,10 +72650,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_27 = __pyx_v_i; + __pyx_t_28 = __pyx_v_j; + __pyx_t_29 = 1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_27 * __pyx_v_g.strides[0]) ) + __pyx_t_28 * __pyx_v_g.strides[1]) ) + __pyx_t_29 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -72581,9 +72662,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_30 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -72602,25 +72683,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -72629,10 +72710,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_j; + __pyx_t_34 = 0; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -72641,10 +72722,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_35 = __pyx_v_i; + __pyx_t_36 = __pyx_v_j; + __pyx_t_37 = 1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_35 * __pyx_v_g.strides[0]) ) + __pyx_t_36 * __pyx_v_g.strides[1]) ) + __pyx_t_37 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -72653,9 +72734,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_38 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_39 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -72674,25 +72755,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -72701,9 +72782,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_244phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_40 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_41 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -72769,6 +72850,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_247phase_progeny_by_tra static PyMethodDef __pyx_fuse_5__pyx_mdef_5allel_3opt_5stats_247phase_progeny_by_transmission = {"__pyx_fuse_5phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_247phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_247phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -72819,21 +72903,21 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + int __pyx_t_13; + int __pyx_t_14; + size_t __pyx_t_15; + size_t __pyx_t_16; + size_t __pyx_t_17; + size_t __pyx_t_18; Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - size_t __pyx_t_24; - size_t __pyx_t_25; - size_t __pyx_t_26; - size_t __pyx_t_27; + size_t __pyx_t_22; + Py_ssize_t __pyx_t_23; + Py_ssize_t __pyx_t_24; + Py_ssize_t __pyx_t_25; + Py_ssize_t __pyx_t_26; + Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; @@ -72843,42 +72927,14 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; Py_ssize_t __pyx_t_36; - size_t __pyx_t_37; - size_t __pyx_t_38; + Py_ssize_t __pyx_t_37; + Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - size_t __pyx_t_41; - size_t __pyx_t_42; - size_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - size_t __pyx_t_46; - size_t __pyx_t_47; - size_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - size_t __pyx_t_68; - size_t __pyx_t_69; - size_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + Py_ssize_t __pyx_t_41; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_5phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -73099,10 +73155,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -73111,10 +73167,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -73123,10 +73179,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -73135,28 +73191,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -73227,8 +73283,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_15 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -73237,8 +73293,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_16 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_16 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -73247,8 +73303,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_17 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_17 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -73257,8 +73313,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_18 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_18 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -73267,10 +73323,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_19 = (__pyx_v_n_progeny + 2); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 2; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_j = __pyx_t_21; /* "allel/opt/stats.pyx":941 * @@ -73279,10 +73335,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_12 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -73291,10 +73347,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_10 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -73303,16 +73359,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -73339,8 +73395,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -73349,18 +73405,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -73369,9 +73425,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_10 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_11 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -73400,25 +73456,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -73427,9 +73483,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_23 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_12 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_23 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -73448,25 +73504,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -73475,10 +73531,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_24 = __pyx_v_i; + __pyx_t_25 = __pyx_v_j; + __pyx_t_26 = 0; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_24 * __pyx_v_g.strides[0]) ) + __pyx_t_25 * __pyx_v_g.strides[1]) ) + __pyx_t_26 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -73487,10 +73543,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_27 = __pyx_v_i; + __pyx_t_28 = __pyx_v_j; + __pyx_t_29 = 1; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_27 * __pyx_v_g.strides[0]) ) + __pyx_t_28 * __pyx_v_g.strides[1]) ) + __pyx_t_29 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -73499,9 +73555,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_30 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -73520,25 +73576,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -73547,10 +73603,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_j; + __pyx_t_34 = 0; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -73559,10 +73615,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_35 = __pyx_v_i; + __pyx_t_36 = __pyx_v_j; + __pyx_t_37 = 1; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_35 * __pyx_v_g.strides[0]) ) + __pyx_t_36 * __pyx_v_g.strides[1]) ) + __pyx_t_37 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -73571,9 +73627,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_38 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_39 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -73592,25 +73648,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -73619,9 +73675,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_246phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_40 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_41 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -73687,6 +73743,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_249phase_progeny_by_tra static PyMethodDef __pyx_fuse_6__pyx_mdef_5allel_3opt_5stats_249phase_progeny_by_transmission = {"__pyx_fuse_6phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_249phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_249phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -73737,21 +73796,21 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + int __pyx_t_13; + int __pyx_t_14; + size_t __pyx_t_15; + size_t __pyx_t_16; + size_t __pyx_t_17; + size_t __pyx_t_18; Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - size_t __pyx_t_24; - size_t __pyx_t_25; - size_t __pyx_t_26; - size_t __pyx_t_27; + size_t __pyx_t_22; + Py_ssize_t __pyx_t_23; + Py_ssize_t __pyx_t_24; + Py_ssize_t __pyx_t_25; + Py_ssize_t __pyx_t_26; + Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; @@ -73761,42 +73820,14 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; Py_ssize_t __pyx_t_36; - size_t __pyx_t_37; - size_t __pyx_t_38; + Py_ssize_t __pyx_t_37; + Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - size_t __pyx_t_41; - size_t __pyx_t_42; - size_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - size_t __pyx_t_46; - size_t __pyx_t_47; - size_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - size_t __pyx_t_68; - size_t __pyx_t_69; - size_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + Py_ssize_t __pyx_t_41; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_6phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -74017,10 +74048,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -74029,10 +74060,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -74041,10 +74072,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -74053,28 +74084,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -74145,8 +74176,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_15 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -74155,8 +74186,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_16 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_16 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -74165,8 +74196,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_17 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_17 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -74175,8 +74206,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_18 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_18 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -74185,10 +74216,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_19 = (__pyx_v_n_progeny + 2); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 2; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_j = __pyx_t_21; /* "allel/opt/stats.pyx":941 * @@ -74197,10 +74228,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_12 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -74209,10 +74240,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_10 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -74221,16 +74252,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -74257,8 +74288,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -74267,18 +74298,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -74287,9 +74318,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_10 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_11 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -74318,25 +74349,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -74345,9 +74376,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_23 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_12 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_23 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -74366,25 +74397,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -74393,10 +74424,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_24 = __pyx_v_i; + __pyx_t_25 = __pyx_v_j; + __pyx_t_26 = 0; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_24 * __pyx_v_g.strides[0]) ) + __pyx_t_25 * __pyx_v_g.strides[1]) ) + __pyx_t_26 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -74405,10 +74436,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_27 = __pyx_v_i; + __pyx_t_28 = __pyx_v_j; + __pyx_t_29 = 1; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_27 * __pyx_v_g.strides[0]) ) + __pyx_t_28 * __pyx_v_g.strides[1]) ) + __pyx_t_29 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -74417,9 +74448,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_30 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -74438,25 +74469,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -74465,10 +74496,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_j; + __pyx_t_34 = 0; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -74477,10 +74508,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_35 = __pyx_v_i; + __pyx_t_36 = __pyx_v_j; + __pyx_t_37 = 1; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_35 * __pyx_v_g.strides[0]) ) + __pyx_t_36 * __pyx_v_g.strides[1]) ) + __pyx_t_37 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -74489,9 +74520,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_38 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_39 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -74510,25 +74541,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -74537,9 +74568,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_248phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_40 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_41 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -74605,6 +74636,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_251phase_progeny_by_tra static PyMethodDef __pyx_fuse_7__pyx_mdef_5allel_3opt_5stats_251phase_progeny_by_transmission = {"__pyx_fuse_7phase_progeny_by_transmission", (PyCFunction)__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_251phase_progeny_by_transmission, METH_O, 0}; static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_251phase_progeny_by_transmission(PyObject *__pyx_self, PyObject *__pyx_arg_g) { __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_progeny_by_transmission (wrapper)", 0); @@ -74655,21 +74689,21 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_10; Py_ssize_t __pyx_t_11; Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; - Py_ssize_t __pyx_t_18; + int __pyx_t_13; + int __pyx_t_14; + __pyx_t_5numpy_uint64_t __pyx_t_15; + __pyx_t_5numpy_uint64_t __pyx_t_16; + __pyx_t_5numpy_uint64_t __pyx_t_17; + __pyx_t_5numpy_uint64_t __pyx_t_18; Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - __pyx_t_5numpy_uint64_t __pyx_t_24; - __pyx_t_5numpy_uint64_t __pyx_t_25; - __pyx_t_5numpy_uint64_t __pyx_t_26; - __pyx_t_5numpy_uint64_t __pyx_t_27; + __pyx_t_5numpy_uint64_t __pyx_t_22; + Py_ssize_t __pyx_t_23; + Py_ssize_t __pyx_t_24; + Py_ssize_t __pyx_t_25; + Py_ssize_t __pyx_t_26; + Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; Py_ssize_t __pyx_t_29; Py_ssize_t __pyx_t_30; @@ -74679,42 +74713,14 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; Py_ssize_t __pyx_t_36; - __pyx_t_5numpy_uint64_t __pyx_t_37; - __pyx_t_5numpy_uint64_t __pyx_t_38; + Py_ssize_t __pyx_t_37; + Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; Py_ssize_t __pyx_t_40; - __pyx_t_5numpy_uint64_t __pyx_t_41; - __pyx_t_5numpy_uint64_t __pyx_t_42; - __pyx_t_5numpy_uint64_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - __pyx_t_5numpy_uint64_t __pyx_t_46; - __pyx_t_5numpy_uint64_t __pyx_t_47; - __pyx_t_5numpy_uint64_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - __pyx_t_5numpy_uint64_t __pyx_t_57; - __pyx_t_5numpy_uint64_t __pyx_t_58; - __pyx_t_5numpy_uint64_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - __pyx_t_5numpy_uint64_t __pyx_t_68; - __pyx_t_5numpy_uint64_t __pyx_t_69; - __pyx_t_5numpy_uint64_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + Py_ssize_t __pyx_t_41; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7phase_progeny_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_7phase_progeny_by_transmission", __pyx_f[0], 892, 0, __PYX_ERR(0, 892, __pyx_L1_error)); @@ -74935,10 +74941,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * pa1 = g[i, 1, 0] # paternal allele 1 * pa2 = g[i, 1, 1] # paternal allele 2 */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_14 = 0; - __pyx_t_15 = 1; - __pyx_v_ma2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_13 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_15 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 0; + __pyx_t_10 = 1; + __pyx_v_ma2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":922 * ma1 = g[i, 0, 0] # maternal allele 1 @@ -74947,10 +74953,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * pa2 = g[i, 1, 1] # paternal allele 2 * */ - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = 1; - __pyx_t_18 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_16 * __pyx_v_g.strides[0]) ) + __pyx_t_17 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_12 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":923 * ma2 = g[i, 0, 1] # maternal allele 2 @@ -74959,10 +74965,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * # check for any missing calls in parents */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 1; - __pyx_t_21 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = 1; + __pyx_t_10 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":926 * @@ -74971,28 +74977,28 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_ma1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_ma2 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_ma2 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_pa1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L6_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_pa2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_pa2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L6_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":927 * # check for any missing calls in parents @@ -75063,8 +75069,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * mac[ma2] = 1 * pac[pa1] = 1 */ - __pyx_t_24 = __pyx_v_ma1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_24 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_15 = __pyx_v_ma1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_15 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":933 * pac[:] = 0 # reset to zero @@ -75073,8 +75079,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * pac[pa1] = 1 * pac[pa2] = 1 */ - __pyx_t_25 = __pyx_v_ma2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_25 * __pyx_v_mac.strides[0]) )) = 1; + __pyx_t_16 = __pyx_v_ma2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_16 * __pyx_v_mac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":934 * mac[ma1] = 1 @@ -75083,8 +75089,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * pac[pa2] = 1 * */ - __pyx_t_26 = __pyx_v_pa1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_26 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_17 = __pyx_v_pa1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_17 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":935 * mac[ma2] = 1 @@ -75093,8 +75099,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * # iterate over progeny */ - __pyx_t_27 = __pyx_v_pa2; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_27 * __pyx_v_pac.strides[0]) )) = 1; + __pyx_t_18 = __pyx_v_pa2; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_18 * __pyx_v_pac.strides[0]) )) = 1; /* "allel/opt/stats.pyx":938 * @@ -75103,10 +75109,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * # access progeny alleles */ - __pyx_t_28 = (__pyx_v_n_progeny + 2); - __pyx_t_29 = __pyx_t_28; - for (__pyx_t_30 = 2; __pyx_t_30 < __pyx_t_29; __pyx_t_30+=1) { - __pyx_v_j = __pyx_t_30; + __pyx_t_19 = (__pyx_v_n_progeny + 2); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 2; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_j = __pyx_t_21; /* "allel/opt/stats.pyx":941 * @@ -75115,10 +75121,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * a2 = g[i, j, 1] * */ - __pyx_t_31 = __pyx_v_i; - __pyx_t_32 = __pyx_v_j; - __pyx_t_33 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_31 * __pyx_v_g.strides[0]) ) + __pyx_t_32 * __pyx_v_g.strides[1]) ) + __pyx_t_33 * __pyx_v_g.strides[2]) ))); + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_12 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_10 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_12 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":942 * # access progeny alleles @@ -75127,10 +75133,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * if a1 < 0 or a2 < 0: # child is missing */ - __pyx_t_34 = __pyx_v_i; - __pyx_t_35 = __pyx_v_j; - __pyx_t_36 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) ))); + __pyx_t_12 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + __pyx_t_10 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_12 * __pyx_v_g.strides[0]) ) + __pyx_t_11 * __pyx_v_g.strides[1]) ) + __pyx_t_10 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":944 * a2 = g[i, j, 1] @@ -75139,16 +75145,16 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * continue * */ - __pyx_t_23 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_23) { + __pyx_t_14 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L13_bool_binop_done; } - __pyx_t_23 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_14 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L13_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":945 * @@ -75175,8 +75181,8 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent */ - __pyx_t_22 = ((__pyx_v_a1 == __pyx_v_a2) != 0); - if (__pyx_t_22) { + __pyx_t_13 = ((__pyx_v_a1 == __pyx_v_a2) != 0); + if (__pyx_t_13) { /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -75185,18 +75191,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * # trivially phase the child * is_phased[i, j] = 1 */ - __pyx_t_37 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_37 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L16_bool_binop_done; } - __pyx_t_38 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_38 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L16_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":951 * if mac[a1] > 0 and pac[a1] > 0: # Mendelian consistent @@ -75205,9 +75211,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * else: # child is heterozygous */ - __pyx_t_39 = __pyx_v_i; - __pyx_t_40 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_39 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_40 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_10 = __pyx_v_i; + __pyx_t_11 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_10 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_11 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":949 * elif a1 == a2: # child is homozygous @@ -75236,25 +75242,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * is_phased[i, j] = 1 */ /*else*/ { - __pyx_t_41 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_41 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_42 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_42 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L19_bool_binop_done; } - __pyx_t_43 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_43 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L19_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":957 * if mac[a1] > 0 and pac[a1] == 0 and pac[a2] > 0: @@ -75263,9 +75269,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: */ - __pyx_t_44 = __pyx_v_i; - __pyx_t_45 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_44 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_45 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_12 = __pyx_v_i; + __pyx_t_23 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_12 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_23 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":955 * else: # child is heterozygous @@ -75284,25 +75290,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * # allele 2 is unique to mother, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_46 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_46 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_47 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_47 * __pyx_v_pac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L22_bool_binop_done; } - __pyx_t_48 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_48 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L22_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":961 * elif mac[a2] > 0 and pac[a2] == 0 and pac[a1] > 0: @@ -75311,10 +75317,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_49 = __pyx_v_i; - __pyx_t_50 = __pyx_v_j; - __pyx_t_51 = 0; - *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_49 * __pyx_v_g.strides[0]) ) + __pyx_t_50 * __pyx_v_g.strides[1]) ) + __pyx_t_51 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_24 = __pyx_v_i; + __pyx_t_25 = __pyx_v_j; + __pyx_t_26 = 0; + *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_24 * __pyx_v_g.strides[0]) ) + __pyx_t_25 * __pyx_v_g.strides[1]) ) + __pyx_t_26 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":962 * # allele 2 is unique to mother, swap child alleles @@ -75323,10 +75329,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_52 = __pyx_v_i; - __pyx_t_53 = __pyx_v_j; - __pyx_t_54 = 1; - *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_52 * __pyx_v_g.strides[0]) ) + __pyx_t_53 * __pyx_v_g.strides[1]) ) + __pyx_t_54 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_27 = __pyx_v_i; + __pyx_t_28 = __pyx_v_j; + __pyx_t_29 = 1; + *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_27 * __pyx_v_g.strides[0]) ) + __pyx_t_28 * __pyx_v_g.strides[1]) ) + __pyx_t_29 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":963 * g[i, j, 0] = a2 @@ -75335,9 +75341,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: */ - __pyx_t_55 = __pyx_v_i; - __pyx_t_56 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_55 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_56 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_30 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":959 * is_phased[i, j] = 1 @@ -75356,25 +75362,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * # allele 1 is unique to father, swap child alleles * g[i, j, 0] = a2 */ - __pyx_t_57 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_57 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_58 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_58 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L25_bool_binop_done; } - __pyx_t_59 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_59 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L25_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":967 * elif pac[a1] > 0 and mac[a1] == 0 and mac[a2] > 0: @@ -75383,10 +75389,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * g[i, j, 1] = a1 * is_phased[i, j] = 1 */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_j; - __pyx_t_62 = 0; - *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_60 * __pyx_v_g.strides[0]) ) + __pyx_t_61 * __pyx_v_g.strides[1]) ) + __pyx_t_62 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_j; + __pyx_t_34 = 0; + *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":968 * # allele 1 is unique to father, swap child alleles @@ -75395,10 +75401,10 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * is_phased[i, j] = 1 * */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_j; - __pyx_t_65 = 1; - *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_63 * __pyx_v_g.strides[0]) ) + __pyx_t_64 * __pyx_v_g.strides[1]) ) + __pyx_t_65 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_35 = __pyx_v_i; + __pyx_t_36 = __pyx_v_j; + __pyx_t_37 = 1; + *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_35 * __pyx_v_g.strides[0]) ) + __pyx_t_36 * __pyx_v_g.strides[1]) ) + __pyx_t_37 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":969 * g[i, j, 0] = a2 @@ -75407,9 +75413,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_66 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_67 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_38 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_39 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":965 * is_phased[i, j] = 1 @@ -75428,25 +75434,25 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * # allele 2 is unique to father, no need to swap * is_phased[i, j] = 1 */ - __pyx_t_68 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_68 * __pyx_v_pac.strides[0]) ))) > 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_pac.data + __pyx_t_22 * __pyx_v_pac.strides[0]) ))) > 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_69 = __pyx_v_a2; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_69 * __pyx_v_mac.strides[0]) ))) == 0) != 0); - if (__pyx_t_23) { + __pyx_t_22 = __pyx_v_a2; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) == 0) != 0); + if (__pyx_t_14) { } else { - __pyx_t_22 = __pyx_t_23; + __pyx_t_13 = __pyx_t_14; goto __pyx_L28_bool_binop_done; } - __pyx_t_70 = __pyx_v_a1; - __pyx_t_23 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_70 * __pyx_v_mac.strides[0]) ))) > 0) != 0); - __pyx_t_22 = __pyx_t_23; + __pyx_t_22 = __pyx_v_a1; + __pyx_t_14 = (((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_mac.data + __pyx_t_22 * __pyx_v_mac.strides[0]) ))) > 0) != 0); + __pyx_t_13 = __pyx_t_14; __pyx_L28_bool_binop_done:; - if (__pyx_t_22) { + if (__pyx_t_13) { /* "allel/opt/stats.pyx":973 * elif pac[a2] > 0 and mac[a2] == 0 and mac[a1] > 0: @@ -75455,9 +75461,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_250phase_progeny_by_transmission(CY * * return is_phased */ - __pyx_t_71 = __pyx_v_i; - __pyx_t_72 = __pyx_v_j; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_71 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_72 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_40 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_41 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":971 * is_phased[i, j] = 1 @@ -75534,6 +75540,9 @@ static PyObject *__pyx_pw_5allel_3opt_5stats_35phase_parents_by_transmission(PyO PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; CYTHON_UNUSED PyObject *__pyx_v_defaults = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__pyx_fused_cpdef (wrapper)", 0); @@ -75655,6 +75664,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_34phase_parents_by_transmission(CYT Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; int __pyx_t_18; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("phase_parents_by_transmission", 0); __Pyx_TraceCall("phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); __Pyx_INCREF(__pyx_v_kwargs); @@ -76358,6 +76370,9 @@ static PyObject *__pyx_fuse_0__pyx_pw_5allel_3opt_5stats_255phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -76464,13 +76479,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_254phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; + Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; @@ -76481,43 +76496,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_254phase_parents_by_transmission(CY Py_ssize_t __pyx_t_33; Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - Py_ssize_t __pyx_t_38; - Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_0phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_0phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -76801,9 +76782,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -76831,10 +76812,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -76843,10 +76824,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -76855,14 +76836,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -76901,9 +76882,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -76922,8 +76903,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -76962,14 +76943,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -76980,10 +76961,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -76992,10 +76973,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -77004,12 +76985,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -77020,10 +77001,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -77034,9 +77015,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -77094,10 +77075,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -77106,18 +77087,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -77128,10 +77109,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -77140,10 +77121,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -77152,9 +77133,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_20 = __pyx_v_x; + __pyx_t_18 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_20 * __pyx_v_linkage.strides[0]) ) + __pyx_t_18 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -77173,11 +77154,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_21 = __pyx_v_pa1; + __pyx_t_25 = __pyx_v_a1; + __pyx_t_26 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_21 * __pyx_v_linkage.strides[0]) ) + __pyx_t_25 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_26 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -77186,11 +77167,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_26 = __pyx_v_a2; + __pyx_t_25 = __pyx_v_pa2; + __pyx_t_21 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_21 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -77228,9 +77209,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_25 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_25 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -77259,9 +77240,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -77290,9 +77271,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_28 = __pyx_v_i; + __pyx_t_29 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_28 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_29 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -77301,10 +77282,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + __pyx_t_32 = 0; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_30 * __pyx_v_g.strides[0]) ) + __pyx_t_31 * __pyx_v_g.strides[1]) ) + __pyx_t_32 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -77313,10 +77294,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_33 = __pyx_v_i; + __pyx_t_34 = __pyx_v_parent; + __pyx_t_35 = 1; + *((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_33 * __pyx_v_g.strides[0]) ) + __pyx_t_34 * __pyx_v_g.strides[1]) ) + __pyx_t_35 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -77382,6 +77363,9 @@ static PyObject *__pyx_fuse_1__pyx_pw_5allel_3opt_5stats_257phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -77488,13 +77472,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_256phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; + Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; @@ -77505,43 +77489,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_256phase_parents_by_transmission(CY Py_ssize_t __pyx_t_33; Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - Py_ssize_t __pyx_t_38; - Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_1phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_1phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -77825,9 +77775,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -77855,10 +77805,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -77867,10 +77817,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -77879,14 +77829,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -77925,9 +77875,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -77946,8 +77896,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -77986,14 +77936,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -78004,10 +77954,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -78016,10 +77966,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -78028,12 +77978,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -78044,10 +77994,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -78058,9 +78008,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -78118,10 +78068,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -78130,18 +78080,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -78152,10 +78102,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -78164,10 +78114,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -78176,9 +78126,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_20 = __pyx_v_x; + __pyx_t_18 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_20 * __pyx_v_linkage.strides[0]) ) + __pyx_t_18 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -78197,11 +78147,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_21 = __pyx_v_pa1; + __pyx_t_25 = __pyx_v_a1; + __pyx_t_26 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_21 * __pyx_v_linkage.strides[0]) ) + __pyx_t_25 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_26 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -78210,11 +78160,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_26 = __pyx_v_a2; + __pyx_t_25 = __pyx_v_pa2; + __pyx_t_21 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_21 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -78252,9 +78202,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_25 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_25 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -78283,9 +78233,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -78314,9 +78264,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_28 = __pyx_v_i; + __pyx_t_29 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_28 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_29 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -78325,10 +78275,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + __pyx_t_32 = 0; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_30 * __pyx_v_g.strides[0]) ) + __pyx_t_31 * __pyx_v_g.strides[1]) ) + __pyx_t_32 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -78337,10 +78287,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_33 = __pyx_v_i; + __pyx_t_34 = __pyx_v_parent; + __pyx_t_35 = 1; + *((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_33 * __pyx_v_g.strides[0]) ) + __pyx_t_34 * __pyx_v_g.strides[1]) ) + __pyx_t_35 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -78406,6 +78356,9 @@ static PyObject *__pyx_fuse_2__pyx_pw_5allel_3opt_5stats_259phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -78512,13 +78465,13 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_258phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; + Py_ssize_t __pyx_t_25; Py_ssize_t __pyx_t_26; Py_ssize_t __pyx_t_27; Py_ssize_t __pyx_t_28; @@ -78529,43 +78482,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_258phase_parents_by_transmission(CY Py_ssize_t __pyx_t_33; Py_ssize_t __pyx_t_34; Py_ssize_t __pyx_t_35; - Py_ssize_t __pyx_t_36; - Py_ssize_t __pyx_t_37; - Py_ssize_t __pyx_t_38; - Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - Py_ssize_t __pyx_t_51; - Py_ssize_t __pyx_t_52; - Py_ssize_t __pyx_t_53; - Py_ssize_t __pyx_t_54; - Py_ssize_t __pyx_t_55; - Py_ssize_t __pyx_t_56; - Py_ssize_t __pyx_t_57; - Py_ssize_t __pyx_t_58; - Py_ssize_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_2phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_2phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -78849,9 +78768,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -78879,10 +78798,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -78891,10 +78810,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -78903,14 +78822,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -78949,9 +78868,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -78970,8 +78889,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -79010,14 +78929,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -79028,10 +78947,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -79040,10 +78959,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -79052,12 +78971,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -79068,10 +78987,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -79082,9 +79001,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -79142,10 +79061,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -79154,18 +79073,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -79176,10 +79095,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -79188,10 +79107,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -79200,9 +79119,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_20 = __pyx_v_x; + __pyx_t_18 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_20 * __pyx_v_linkage.strides[0]) ) + __pyx_t_18 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -79221,11 +79140,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_21 = __pyx_v_pa1; + __pyx_t_25 = __pyx_v_a1; + __pyx_t_26 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_21 * __pyx_v_linkage.strides[0]) ) + __pyx_t_25 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_26 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -79234,11 +79153,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_26 = __pyx_v_a2; + __pyx_t_25 = __pyx_v_pa2; + __pyx_t_21 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_21 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -79276,9 +79195,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_25 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_25 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -79307,9 +79226,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -79338,9 +79257,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_28 = __pyx_v_i; + __pyx_t_29 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_28 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_29 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -79349,10 +79268,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + __pyx_t_32 = 0; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_30 * __pyx_v_g.strides[0]) ) + __pyx_t_31 * __pyx_v_g.strides[1]) ) + __pyx_t_32 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -79361,10 +79280,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_33 = __pyx_v_i; + __pyx_t_34 = __pyx_v_parent; + __pyx_t_35 = 1; + *((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_33 * __pyx_v_g.strides[0]) ) + __pyx_t_34 * __pyx_v_g.strides[1]) ) + __pyx_t_35 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -79430,6 +79349,9 @@ static PyObject *__pyx_fuse_3__pyx_pw_5allel_3opt_5stats_261phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -79536,17 +79458,17 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_260phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; + __pyx_t_5numpy_int64_t __pyx_t_25; + __pyx_t_5numpy_int64_t __pyx_t_26; + __pyx_t_5numpy_int64_t __pyx_t_27; + __pyx_t_5numpy_int64_t __pyx_t_28; + __pyx_t_5numpy_int64_t __pyx_t_29; Py_ssize_t __pyx_t_30; Py_ssize_t __pyx_t_31; Py_ssize_t __pyx_t_32; @@ -79556,39 +79478,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_260phase_parents_by_transmission(CY Py_ssize_t __pyx_t_36; Py_ssize_t __pyx_t_37; Py_ssize_t __pyx_t_38; - Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - __pyx_t_5numpy_int64_t __pyx_t_51; - __pyx_t_5numpy_int64_t __pyx_t_52; - __pyx_t_5numpy_int64_t __pyx_t_53; - __pyx_t_5numpy_int64_t __pyx_t_54; - __pyx_t_5numpy_int64_t __pyx_t_55; - __pyx_t_5numpy_int64_t __pyx_t_56; - __pyx_t_5numpy_int64_t __pyx_t_57; - __pyx_t_5numpy_int64_t __pyx_t_58; - __pyx_t_5numpy_int64_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_3phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_3phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -79872,9 +79764,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -79902,10 +79794,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -79914,10 +79806,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -79926,14 +79818,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -79972,9 +79864,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -79993,8 +79885,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -80033,14 +79925,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -80051,10 +79943,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -80063,10 +79955,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -80075,12 +79967,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -80091,10 +79983,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -80105,9 +79997,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -80165,10 +80057,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -80177,18 +80069,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -80199,10 +80091,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -80211,10 +80103,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -80224,8 +80116,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # accumulate evidence */ __pyx_t_5 = __pyx_v_x; - __pyx_t_51 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_5 * __pyx_v_linkage.strides[0]) ) + __pyx_t_51 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_25 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_5 * __pyx_v_linkage.strides[0]) ) + __pyx_t_25 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -80244,11 +80136,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_52 = __pyx_v_pa1; - __pyx_t_53 = __pyx_v_a1; - __pyx_t_54 = __pyx_v_pa2; - __pyx_t_55 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_52 * __pyx_v_linkage.strides[0]) ) + __pyx_t_53 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_54 * __pyx_v_linkage.strides[0]) ) + __pyx_t_55 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_26 = __pyx_v_pa1; + __pyx_t_27 = __pyx_v_a1; + __pyx_t_28 = __pyx_v_pa2; + __pyx_t_29 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_26 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_28 * __pyx_v_linkage.strides[0]) ) + __pyx_t_29 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -80257,11 +80149,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_56 = __pyx_v_pa1; - __pyx_t_57 = __pyx_v_a2; - __pyx_t_58 = __pyx_v_pa2; - __pyx_t_59 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_56 * __pyx_v_linkage.strides[0]) ) + __pyx_t_57 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_58 * __pyx_v_linkage.strides[0]) ) + __pyx_t_59 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_29 = __pyx_v_pa1; + __pyx_t_28 = __pyx_v_a2; + __pyx_t_27 = __pyx_v_pa2; + __pyx_t_26 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_29 * __pyx_v_linkage.strides[0]) ) + __pyx_t_28 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -80299,9 +80191,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_60 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_61 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_20 = __pyx_v_i; + __pyx_t_18 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -80330,9 +80222,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_62 = __pyx_v_i; - __pyx_t_63 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_62 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_63 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_30 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_30 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -80361,9 +80253,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_64 = __pyx_v_i; - __pyx_t_65 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_64 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_65 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_31 = __pyx_v_i; + __pyx_t_32 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_31 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_32 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -80372,10 +80264,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_parent; - __pyx_t_68 = 0; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_66 * __pyx_v_g.strides[0]) ) + __pyx_t_67 * __pyx_v_g.strides[1]) ) + __pyx_t_68 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_33 = __pyx_v_i; + __pyx_t_34 = __pyx_v_parent; + __pyx_t_35 = 0; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_33 * __pyx_v_g.strides[0]) ) + __pyx_t_34 * __pyx_v_g.strides[1]) ) + __pyx_t_35 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -80384,10 +80276,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_69 = __pyx_v_i; - __pyx_t_70 = __pyx_v_parent; - __pyx_t_71 = 1; - *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_69 * __pyx_v_g.strides[0]) ) + __pyx_t_70 * __pyx_v_g.strides[1]) ) + __pyx_t_71 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_36 = __pyx_v_i; + __pyx_t_37 = __pyx_v_parent; + __pyx_t_38 = 1; + *((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_36 * __pyx_v_g.strides[0]) ) + __pyx_t_37 * __pyx_v_g.strides[1]) ) + __pyx_t_38 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -80453,6 +80345,9 @@ static PyObject *__pyx_fuse_4__pyx_pw_5allel_3opt_5stats_263phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -80559,18 +80454,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_262phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; + size_t __pyx_t_25; + size_t __pyx_t_26; + size_t __pyx_t_27; + size_t __pyx_t_28; + size_t __pyx_t_29; + size_t __pyx_t_30; Py_ssize_t __pyx_t_31; Py_ssize_t __pyx_t_32; Py_ssize_t __pyx_t_33; @@ -80580,39 +80475,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_262phase_parents_by_transmission(CY Py_ssize_t __pyx_t_37; Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - size_t __pyx_t_51; - size_t __pyx_t_52; - size_t __pyx_t_53; - size_t __pyx_t_54; - size_t __pyx_t_55; - size_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - size_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_4phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_4phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -80896,9 +80761,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -80926,10 +80791,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -80938,10 +80803,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -80950,14 +80815,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -80996,9 +80861,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -81017,8 +80882,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -81057,14 +80922,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -81075,10 +80940,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -81087,10 +80952,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -81099,12 +80964,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -81115,10 +80980,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -81129,9 +80994,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -81189,10 +81054,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -81201,18 +81066,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -81223,10 +81088,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -81235,10 +81100,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -81247,9 +81112,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_25 = __pyx_v_x; + __pyx_t_26 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -81268,11 +81133,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_28 = __pyx_v_a1; + __pyx_t_29 = __pyx_v_pa2; + __pyx_t_30 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_28 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_29 * __pyx_v_linkage.strides[0]) ) + __pyx_t_30 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -81281,11 +81146,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_30 = __pyx_v_pa1; + __pyx_t_29 = __pyx_v_a2; + __pyx_t_28 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_30 * __pyx_v_linkage.strides[0]) ) + __pyx_t_29 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_28 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -81323,9 +81188,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_20 = __pyx_v_i; + __pyx_t_18 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -81354,9 +81219,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -81385,9 +81250,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_32 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_33 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -81396,10 +81261,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_parent; + __pyx_t_36 = 0; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -81408,10 +81273,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_parent; + __pyx_t_39 = 1; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_37 * __pyx_v_g.strides[0]) ) + __pyx_t_38 * __pyx_v_g.strides[1]) ) + __pyx_t_39 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -81477,6 +81342,9 @@ static PyObject *__pyx_fuse_5__pyx_pw_5allel_3opt_5stats_265phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -81583,18 +81451,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_264phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; + size_t __pyx_t_25; + size_t __pyx_t_26; + size_t __pyx_t_27; + size_t __pyx_t_28; + size_t __pyx_t_29; + size_t __pyx_t_30; Py_ssize_t __pyx_t_31; Py_ssize_t __pyx_t_32; Py_ssize_t __pyx_t_33; @@ -81604,39 +81472,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_264phase_parents_by_transmission(CY Py_ssize_t __pyx_t_37; Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - size_t __pyx_t_51; - size_t __pyx_t_52; - size_t __pyx_t_53; - size_t __pyx_t_54; - size_t __pyx_t_55; - size_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - size_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_5phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_5phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -81920,9 +81758,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -81950,10 +81788,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -81962,10 +81800,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -81974,14 +81812,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -82020,9 +81858,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -82041,8 +81879,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -82081,14 +81919,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -82099,10 +81937,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -82111,10 +81949,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -82123,12 +81961,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -82139,10 +81977,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -82153,9 +81991,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -82213,10 +82051,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -82225,18 +82063,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -82247,10 +82085,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -82259,10 +82097,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -82271,9 +82109,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_25 = __pyx_v_x; + __pyx_t_26 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -82292,11 +82130,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_28 = __pyx_v_a1; + __pyx_t_29 = __pyx_v_pa2; + __pyx_t_30 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_28 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_29 * __pyx_v_linkage.strides[0]) ) + __pyx_t_30 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -82305,11 +82143,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_30 = __pyx_v_pa1; + __pyx_t_29 = __pyx_v_a2; + __pyx_t_28 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_30 * __pyx_v_linkage.strides[0]) ) + __pyx_t_29 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_28 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -82347,9 +82185,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_20 = __pyx_v_i; + __pyx_t_18 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -82378,9 +82216,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -82409,9 +82247,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_32 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_33 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -82420,10 +82258,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_parent; + __pyx_t_36 = 0; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -82432,10 +82270,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_parent; + __pyx_t_39 = 1; + *((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_37 * __pyx_v_g.strides[0]) ) + __pyx_t_38 * __pyx_v_g.strides[1]) ) + __pyx_t_39 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -82501,6 +82339,9 @@ static PyObject *__pyx_fuse_6__pyx_pw_5allel_3opt_5stats_267phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -82607,18 +82448,18 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_266phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; - Py_ssize_t __pyx_t_30; + size_t __pyx_t_25; + size_t __pyx_t_26; + size_t __pyx_t_27; + size_t __pyx_t_28; + size_t __pyx_t_29; + size_t __pyx_t_30; Py_ssize_t __pyx_t_31; Py_ssize_t __pyx_t_32; Py_ssize_t __pyx_t_33; @@ -82628,39 +82469,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_266phase_parents_by_transmission(CY Py_ssize_t __pyx_t_37; Py_ssize_t __pyx_t_38; Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - size_t __pyx_t_51; - size_t __pyx_t_52; - size_t __pyx_t_53; - size_t __pyx_t_54; - size_t __pyx_t_55; - size_t __pyx_t_56; - size_t __pyx_t_57; - size_t __pyx_t_58; - size_t __pyx_t_59; - size_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; - Py_ssize_t __pyx_t_72; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_6phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_6phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -82944,9 +82755,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -82974,10 +82785,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -82986,10 +82797,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -82998,14 +82809,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -83044,9 +82855,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -83065,8 +82876,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -83105,14 +82916,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -83123,10 +82934,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -83135,10 +82946,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -83147,12 +82958,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -83163,10 +82974,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -83177,9 +82988,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -83237,10 +83048,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -83249,18 +83060,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -83271,10 +83082,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -83283,10 +83094,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -83295,9 +83106,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # accumulate evidence */ - __pyx_t_51 = __pyx_v_x; - __pyx_t_52 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_51 * __pyx_v_linkage.strides[0]) ) + __pyx_t_52 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_25 = __pyx_v_x; + __pyx_t_26 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_25 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -83316,11 +83127,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_53 = __pyx_v_pa1; - __pyx_t_54 = __pyx_v_a1; - __pyx_t_55 = __pyx_v_pa2; - __pyx_t_56 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_53 * __pyx_v_linkage.strides[0]) ) + __pyx_t_54 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_55 * __pyx_v_linkage.strides[0]) ) + __pyx_t_56 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_27 = __pyx_v_pa1; + __pyx_t_28 = __pyx_v_a1; + __pyx_t_29 = __pyx_v_pa2; + __pyx_t_30 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_28 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_29 * __pyx_v_linkage.strides[0]) ) + __pyx_t_30 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -83329,11 +83140,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_57 = __pyx_v_pa1; - __pyx_t_58 = __pyx_v_a2; - __pyx_t_59 = __pyx_v_pa2; - __pyx_t_60 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_57 * __pyx_v_linkage.strides[0]) ) + __pyx_t_58 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_59 * __pyx_v_linkage.strides[0]) ) + __pyx_t_60 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_30 = __pyx_v_pa1; + __pyx_t_29 = __pyx_v_a2; + __pyx_t_28 = __pyx_v_pa2; + __pyx_t_27 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_30 * __pyx_v_linkage.strides[0]) ) + __pyx_t_29 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_28 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -83371,9 +83182,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_61 = __pyx_v_i; - __pyx_t_62 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_61 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_62 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_20 = __pyx_v_i; + __pyx_t_18 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -83402,9 +83213,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_63 = __pyx_v_i; - __pyx_t_64 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_63 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_64 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_31 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_31 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -83433,9 +83244,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_65 = __pyx_v_i; - __pyx_t_66 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_65 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_66 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_32 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_33 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -83444,10 +83255,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_67 = __pyx_v_i; - __pyx_t_68 = __pyx_v_parent; - __pyx_t_69 = 0; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_67 * __pyx_v_g.strides[0]) ) + __pyx_t_68 * __pyx_v_g.strides[1]) ) + __pyx_t_69 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_parent; + __pyx_t_36 = 0; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_34 * __pyx_v_g.strides[0]) ) + __pyx_t_35 * __pyx_v_g.strides[1]) ) + __pyx_t_36 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; /* "allel/opt/stats.pyx":1083 * is_phased[i, parent] = 1 @@ -83456,10 +83267,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * */ - __pyx_t_70 = __pyx_v_i; - __pyx_t_71 = __pyx_v_parent; - __pyx_t_72 = 1; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_70 * __pyx_v_g.strides[0]) ) + __pyx_t_71 * __pyx_v_g.strides[1]) ) + __pyx_t_72 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; + __pyx_t_37 = __pyx_v_i; + __pyx_t_38 = __pyx_v_parent; + __pyx_t_39 = 1; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_37 * __pyx_v_g.strides[0]) ) + __pyx_t_38 * __pyx_v_g.strides[1]) ) + __pyx_t_39 * __pyx_v_g.strides[2]) )) = __pyx_v_a1; /* "allel/opt/stats.pyx":1080 * is_phased[i, parent] = 1 @@ -83525,6 +83336,9 @@ static PyObject *__pyx_fuse_7__pyx_pw_5allel_3opt_5stats_269phase_parents_by_tra __Pyx_memviewslice __pyx_v_g = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_is_phased = { 0, 0, { 0 }, { 0 }, { 0 } }; Py_ssize_t __pyx_v_window_size; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("phase_parents_by_transmission (wrapper)", 0); @@ -83631,17 +83445,17 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_268phase_parents_by_transmission(CY Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - Py_ssize_t __pyx_t_19; + int __pyx_t_19; Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; - Py_ssize_t __pyx_t_26; - Py_ssize_t __pyx_t_27; - Py_ssize_t __pyx_t_28; - Py_ssize_t __pyx_t_29; + __pyx_t_5numpy_uint64_t __pyx_t_25; + __pyx_t_5numpy_uint64_t __pyx_t_26; + __pyx_t_5numpy_uint64_t __pyx_t_27; + __pyx_t_5numpy_uint64_t __pyx_t_28; + __pyx_t_5numpy_uint64_t __pyx_t_29; Py_ssize_t __pyx_t_30; Py_ssize_t __pyx_t_31; Py_ssize_t __pyx_t_32; @@ -83651,39 +83465,9 @@ static PyObject *__pyx_pf_5allel_3opt_5stats_268phase_parents_by_transmission(CY Py_ssize_t __pyx_t_36; Py_ssize_t __pyx_t_37; Py_ssize_t __pyx_t_38; - Py_ssize_t __pyx_t_39; - Py_ssize_t __pyx_t_40; - Py_ssize_t __pyx_t_41; - Py_ssize_t __pyx_t_42; - Py_ssize_t __pyx_t_43; - Py_ssize_t __pyx_t_44; - Py_ssize_t __pyx_t_45; - Py_ssize_t __pyx_t_46; - Py_ssize_t __pyx_t_47; - Py_ssize_t __pyx_t_48; - Py_ssize_t __pyx_t_49; - Py_ssize_t __pyx_t_50; - __pyx_t_5numpy_uint64_t __pyx_t_51; - __pyx_t_5numpy_uint64_t __pyx_t_52; - __pyx_t_5numpy_uint64_t __pyx_t_53; - __pyx_t_5numpy_uint64_t __pyx_t_54; - __pyx_t_5numpy_uint64_t __pyx_t_55; - __pyx_t_5numpy_uint64_t __pyx_t_56; - __pyx_t_5numpy_uint64_t __pyx_t_57; - __pyx_t_5numpy_uint64_t __pyx_t_58; - __pyx_t_5numpy_uint64_t __pyx_t_59; - Py_ssize_t __pyx_t_60; - Py_ssize_t __pyx_t_61; - Py_ssize_t __pyx_t_62; - Py_ssize_t __pyx_t_63; - Py_ssize_t __pyx_t_64; - Py_ssize_t __pyx_t_65; - Py_ssize_t __pyx_t_66; - Py_ssize_t __pyx_t_67; - Py_ssize_t __pyx_t_68; - Py_ssize_t __pyx_t_69; - Py_ssize_t __pyx_t_70; - Py_ssize_t __pyx_t_71; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__pyx_fuse_7phase_parents_by_transmission", 0); __Pyx_TraceCall("__pyx_fuse_7phase_parents_by_transmission", __pyx_f[0], 980, 0, __PYX_ERR(0, 980, __pyx_L1_error)); @@ -83967,9 +83751,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent already phased somehow, not expected but skip anyway * continue */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_parent; - __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_14 = __pyx_v_i; + __pyx_t_17 = __pyx_v_parent; + __pyx_t_15 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_14 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_17 * __pyx_v_is_phased.strides[1]) ))) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1016 @@ -83997,10 +83781,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * a2 = g[i, parent, 1] * */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = __pyx_v_parent; - __pyx_t_21 = 0; - __pyx_v_a1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_19 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_18 = 0; + __pyx_v_a1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_17 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1020 * # access parent's alleles @@ -84009,10 +83793,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if a1 < 0 or a2 < 0: */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_parent; - __pyx_t_24 = 1; - __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_22 * __pyx_v_g.strides[0]) ) + __pyx_t_23 * __pyx_v_g.strides[1]) ) + __pyx_t_24 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + __pyx_t_17 = 1; + __pyx_v_a2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_14 * __pyx_v_g.strides[1]) ) + __pyx_t_17 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1022 * a2 = g[i, parent, 1] @@ -84021,14 +83805,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # missing call, skip * continue */ - __pyx_t_25 = ((__pyx_v_a1 < 0) != 0); - if (!__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_a1 < 0) != 0); + if (!__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L10_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_a2 < 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_a2 < 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L10_bool_binop_done:; if (__pyx_t_15) { @@ -84067,9 +83851,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif n_progeny_phased[i] > 0: */ - __pyx_t_26 = __pyx_v_i; - __pyx_t_27 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_26 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_27 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_17 = __pyx_v_i; + __pyx_t_14 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_17 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_14 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1026 * continue @@ -84088,8 +83872,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # parent is het and some progeny are phased, so should be * # able to phase parent */ - __pyx_t_28 = __pyx_v_i; - __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_28 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_18 = __pyx_v_i; + __pyx_t_15 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_18 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); if (__pyx_t_15) { /* "allel/opt/stats.pyx":1035 @@ -84128,14 +83912,14 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # access alleles for previous variant */ while (1) { - __pyx_t_25 = ((__pyx_v_ii >= 0) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_ii >= 0) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L14_bool_binop_done; } - __pyx_t_25 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_19 = ((__pyx_v_n_inf < __pyx_v_window_size) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L14_bool_binop_done:; if (!__pyx_t_15) break; @@ -84146,10 +83930,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * pa2 = g[ii, parent, 1] * */ - __pyx_t_29 = __pyx_v_ii; - __pyx_t_30 = __pyx_v_parent; - __pyx_t_31 = 0; - __pyx_v_pa1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_29 * __pyx_v_g.strides[0]) ) + __pyx_t_30 * __pyx_v_g.strides[1]) ) + __pyx_t_31 * __pyx_v_g.strides[2]) ))); + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_21 = 0; + __pyx_v_pa1 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_18 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1048 * # access alleles for previous variant @@ -84158,10 +83942,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * if (is_phased[ii, parent] and */ - __pyx_t_32 = __pyx_v_ii; - __pyx_t_33 = __pyx_v_parent; - __pyx_t_34 = 1; - __pyx_v_pa2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_32 * __pyx_v_g.strides[0]) ) + __pyx_t_33 * __pyx_v_g.strides[1]) ) + __pyx_t_34 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_18 = 1; + __pyx_v_pa2 = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_20 * __pyx_v_g.strides[1]) ) + __pyx_t_18 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -84170,12 +83954,12 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (pa1 != pa2) and * (n_progeny_phased[ii] > 0)): */ - __pyx_t_35 = __pyx_v_ii; - __pyx_t_36 = __pyx_v_parent; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_35 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_36 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_18 = __pyx_v_ii; + __pyx_t_20 = __pyx_v_parent; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -84186,10 +83970,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * (n_progeny_phased[ii] > 0)): * */ - __pyx_t_25 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); - if (__pyx_t_25) { + __pyx_t_19 = ((__pyx_v_pa1 != __pyx_v_pa2) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L17_bool_binop_done; } @@ -84200,9 +83984,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * # variant is phase informative, accumulate */ - __pyx_t_37 = __pyx_v_ii; - __pyx_t_25 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_37 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_20 = __pyx_v_ii; + __pyx_t_19 = (((*((__pyx_t_5numpy_uint32_t *) ( /* dim=0 */ (__pyx_v_n_progeny_phased.data + __pyx_t_20 * __pyx_v_n_progeny_phased.strides[0]) ))) > 0) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L17_bool_binop_done:; /* "allel/opt/stats.pyx":1050 @@ -84260,10 +84044,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * if is_phased[ii, j] and is_phased[i, j]: * x = g[ii, j, parent] */ - __pyx_t_38 = __pyx_v_n_samples; - __pyx_t_39 = __pyx_t_38; - for (__pyx_t_40 = 2; __pyx_t_40 < __pyx_t_39; __pyx_t_40+=1) { - __pyx_v_j = __pyx_t_40; + __pyx_t_22 = __pyx_v_n_samples; + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 2; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_j = __pyx_t_24; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -84272,18 +84056,18 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * x = g[ii, j, parent] * y = g[i, j, parent] */ - __pyx_t_41 = __pyx_v_ii; - __pyx_t_42 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_41 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_42 * __pyx_v_is_phased.strides[1]) ))) != 0); - if (__pyx_t_25) { + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) ))) != 0); + if (__pyx_t_19) { } else { - __pyx_t_15 = __pyx_t_25; + __pyx_t_15 = __pyx_t_19; goto __pyx_L23_bool_binop_done; } - __pyx_t_43 = __pyx_v_i; - __pyx_t_44 = __pyx_v_j; - __pyx_t_25 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_43 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_44 * __pyx_v_is_phased.strides[1]) ))) != 0); - __pyx_t_15 = __pyx_t_25; + __pyx_t_18 = __pyx_v_i; + __pyx_t_20 = __pyx_v_j; + __pyx_t_19 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_18 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_20 * __pyx_v_is_phased.strides[1]) ))) != 0); + __pyx_t_15 = __pyx_t_19; __pyx_L23_bool_binop_done:; if (__pyx_t_15) { @@ -84294,10 +84078,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * y = g[i, j, parent] * linkage[x, y] += 1 */ - __pyx_t_45 = __pyx_v_ii; - __pyx_t_46 = __pyx_v_j; - __pyx_t_47 = __pyx_v_parent; - __pyx_v_x = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_45 * __pyx_v_g.strides[0]) ) + __pyx_t_46 * __pyx_v_g.strides[1]) ) + __pyx_t_47 * __pyx_v_g.strides[2]) ))); + __pyx_t_20 = __pyx_v_ii; + __pyx_t_18 = __pyx_v_j; + __pyx_t_21 = __pyx_v_parent; + __pyx_v_x = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_20 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_21 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1062 * if is_phased[ii, j] and is_phased[i, j]: @@ -84306,10 +84090,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * linkage[x, y] += 1 * */ - __pyx_t_48 = __pyx_v_i; - __pyx_t_49 = __pyx_v_j; - __pyx_t_50 = __pyx_v_parent; - __pyx_v_y = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_48 * __pyx_v_g.strides[0]) ) + __pyx_t_49 * __pyx_v_g.strides[1]) ) + __pyx_t_50 * __pyx_v_g.strides[2]) ))); + __pyx_t_21 = __pyx_v_i; + __pyx_t_18 = __pyx_v_j; + __pyx_t_20 = __pyx_v_parent; + __pyx_v_y = (*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_21 * __pyx_v_g.strides[0]) ) + __pyx_t_18 * __pyx_v_g.strides[1]) ) + __pyx_t_20 * __pyx_v_g.strides[2]) ))); /* "allel/opt/stats.pyx":1063 * x = g[ii, j, parent] @@ -84319,8 +84103,8 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * # accumulate evidence */ __pyx_t_5 = __pyx_v_x; - __pyx_t_51 = __pyx_v_y; - *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_5 * __pyx_v_linkage.strides[0]) ) + __pyx_t_51 * __pyx_v_linkage.strides[1]) )) += 1; + __pyx_t_25 = __pyx_v_y; + *((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_5 * __pyx_v_linkage.strides[0]) ) + __pyx_t_25 * __pyx_v_linkage.strides[1]) )) += 1; /* "allel/opt/stats.pyx":1060 * linkage[:, :] = 0 @@ -84339,11 +84123,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * flip += linkage[pa1, a2] + linkage[pa2, a1] * */ - __pyx_t_52 = __pyx_v_pa1; - __pyx_t_53 = __pyx_v_a1; - __pyx_t_54 = __pyx_v_pa2; - __pyx_t_55 = __pyx_v_a2; - __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_52 * __pyx_v_linkage.strides[0]) ) + __pyx_t_53 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_54 * __pyx_v_linkage.strides[0]) ) + __pyx_t_55 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_26 = __pyx_v_pa1; + __pyx_t_27 = __pyx_v_a1; + __pyx_t_28 = __pyx_v_pa2; + __pyx_t_29 = __pyx_v_a2; + __pyx_v_keep = (__pyx_v_keep + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_26 * __pyx_v_linkage.strides[0]) ) + __pyx_t_27 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_28 * __pyx_v_linkage.strides[0]) ) + __pyx_t_29 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1067 * # accumulate evidence @@ -84352,11 +84136,11 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * ii -= 1 */ - __pyx_t_56 = __pyx_v_pa1; - __pyx_t_57 = __pyx_v_a2; - __pyx_t_58 = __pyx_v_pa2; - __pyx_t_59 = __pyx_v_a1; - __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_56 * __pyx_v_linkage.strides[0]) ) + __pyx_t_57 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_58 * __pyx_v_linkage.strides[0]) ) + __pyx_t_59 * __pyx_v_linkage.strides[1]) ))))); + __pyx_t_29 = __pyx_v_pa1; + __pyx_t_28 = __pyx_v_a2; + __pyx_t_27 = __pyx_v_pa2; + __pyx_t_26 = __pyx_v_a1; + __pyx_v_flip = (__pyx_v_flip + ((*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_29 * __pyx_v_linkage.strides[0]) ) + __pyx_t_28 * __pyx_v_linkage.strides[1]) ))) + (*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_linkage.data + __pyx_t_27 * __pyx_v_linkage.strides[0]) ) + __pyx_t_26 * __pyx_v_linkage.strides[1]) ))))); /* "allel/opt/stats.pyx":1050 * pa2 = g[ii, parent, 1] @@ -84394,9 +84178,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif keep > flip: */ - __pyx_t_60 = __pyx_v_i; - __pyx_t_61 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_60 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_61 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_20 = __pyx_v_i; + __pyx_t_18 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_20 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_18 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1072 * @@ -84425,9 +84209,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * * elif flip > keep: */ - __pyx_t_62 = __pyx_v_i; - __pyx_t_63 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_62 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_63 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_21 = __pyx_v_i; + __pyx_t_30 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_21 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_30 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1077 * is_phased[i, parent] = 1 @@ -84456,9 +84240,9 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 0] = a2 * g[i, parent, 1] = a1 */ - __pyx_t_64 = __pyx_v_i; - __pyx_t_65 = __pyx_v_parent; - *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_64 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_65 * __pyx_v_is_phased.strides[1]) )) = 1; + __pyx_t_31 = __pyx_v_i; + __pyx_t_32 = __pyx_v_parent; + *((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_is_phased.data + __pyx_t_31 * __pyx_v_is_phased.strides[0]) ) + __pyx_t_32 * __pyx_v_is_phased.strides[1]) )) = 1; /* "allel/opt/stats.pyx":1082 * elif flip > keep: @@ -84467,10 +84251,10 @@ __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_t_7, 2, (PyObject *(*)(char *)) __p * g[i, parent, 1] = a1 * */ - __pyx_t_66 = __pyx_v_i; - __pyx_t_67 = __pyx_v_parent; - __pyx_t_68 = 0; - *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_66 * __pyx_v_g.strides[0]) ) + __pyx_t_67 * __pyx_v_g.strides[1]) ) + __pyx_t_68 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; + __pyx_t_33 = __pyx_v_i; + __pyx_t_34 = __pyx_v_parent; + __pyx_t_35 = 0; + *((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_g.data + __pyx_t_33 * __pyx_v_g.strides[0]) ) + __pyx_t_34 * __pyx_v_g.strides[1]) ) + __pyx_t_35 * __pyx_v_g.strides[2]) )) = __pyx_v_a2; 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int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); @@ -96380,6 +95430,9 @@ static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struc int __pyx_r; __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); __Pyx_TraceCall("__init__", __pyx_f[2], 281, 0, __PYX_ERR(2, 281, __pyx_L1_error)); @@ -96441,6 +95494,9 @@ static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr_ PyObject *__pyx_r = NULL; __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__repr__", 0); __Pyx_TraceCall("__repr__", __pyx_f[2], 283, 0, __PYX_ERR(2, 283, __pyx_L1_error)); @@ -96506,6 +95562,9 @@ static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_Memvi int __pyx_t_3; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__reduce_cython__", 0); __Pyx_TraceCall("__reduce_cython__", __pyx_f[2], 1, 0, __PYX_ERR(2, 1, __pyx_L1_error)); @@ -96734,6 +95793,9 @@ static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_Me __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__setstate_cython__", 0); __Pyx_TraceCall("__setstate_cython__", __pyx_f[2], 16, 0, __PYX_ERR(2, 16, __pyx_L1_error)); @@ -96782,6 +95844,9 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) void *__pyx_r; __Pyx_TraceDeclarations int __pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_TraceCall("align_pointer", __pyx_f[2], 298, 1, __PYX_ERR(2, 298, __pyx_L1_error)); /* "View.MemoryView":300 @@ -96871,6 +95936,9 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar PyObject *__pyx_v_obj = 0; int __pyx_v_flags; int __pyx_v_dtype_is_object; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); @@ -96952,6 +96020,9 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); __Pyx_TraceCall("__cinit__", __pyx_f[2], 345, 0, __PYX_ERR(2, 345, __pyx_L1_error)); @@ -97263,6 +96334,9 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal int __pyx_t_5; PyThread_type_lock __pyx_t_6; PyThread_type_lock __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; 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+ } + + /* "View.MemoryView":375 + * if self.obj is not None: + * __Pyx_ReleaseBuffer(&self.view) + * elif (<__pyx_buffer *> &self.view).obj == Py_None: # <<<<<<<<<<<<<< + * + * (<__pyx_buffer *> &self.view).obj = NULL + */ + __pyx_t_2 = ((((Py_buffer *)(&__pyx_v_self->view))->obj == Py_None) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":377 + * elif (<__pyx_buffer *> &self.view).obj == Py_None: + * + * (<__pyx_buffer *> &self.view).obj = NULL # <<<<<<<<<<<<<< + * Py_DECREF(Py_None) + * + */ + ((Py_buffer *)(&__pyx_v_self->view))->obj = NULL; + + /* "View.MemoryView":378 + * + * (<__pyx_buffer *> &self.view).obj = NULL + * Py_DECREF(Py_None) # <<<<<<<<<<<<<< + * + * cdef int i + */ + Py_DECREF(Py_None); + + /* "View.MemoryView":375 + * if self.obj is not None: + * __Pyx_ReleaseBuffer(&self.view) + * elif (<__pyx_buffer *> &self.view).obj == Py_None: # <<<<<<<<<<<<<< * + * (<__pyx_buffer *> &self.view).obj = NULL */ } + __pyx_L3:; - /* "View.MemoryView":378 + /* "View.MemoryView":382 * cdef int i * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: # <<<<<<<<<<<<<< @@ -97305,7 +96418,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_self->lock != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":379 + /* "View.MemoryView":383 * global __pyx_memoryview_thread_locks_used * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): # <<<<<<<<<<<<<< @@ -97317,7 +96430,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -97327,7 +96440,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = (((__pyx_memoryview_thread_locks[__pyx_v_i]) == __pyx_v_self->lock) != 0); if (__pyx_t_2) { - /* "View.MemoryView":381 + /* "View.MemoryView":385 * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 # <<<<<<<<<<<<<< @@ -97336,7 +96449,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ __pyx_memoryview_thread_locks_used = (__pyx_memoryview_thread_locks_used - 1); 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(__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]) = __pyx_t_7; - /* "View.MemoryView":382 + /* "View.MemoryView":386 * if __pyx_memoryview_thread_locks[i] is self.lock: * __pyx_memoryview_thread_locks_used -= 1 * if i != __pyx_memoryview_thread_locks_used: # <<<<<<<<<<<<<< @@ -97375,7 +96488,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ } - /* "View.MemoryView":385 + /* "View.MemoryView":389 * __pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = ( * __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i]) * break # <<<<<<<<<<<<<< @@ -97384,7 +96497,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal */ goto __pyx_L6_break; - /* "View.MemoryView":380 + /* "View.MemoryView":384 * if self.lock != NULL: * for i in range(__pyx_memoryview_thread_locks_used): * if __pyx_memoryview_thread_locks[i] is self.lock: # <<<<<<<<<<<<<< @@ -97395,7 +96508,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } /*else*/ { - /* "View.MemoryView":387 + /* "View.MemoryView":391 * break * else: * PyThread_free_lock(self.lock) # <<<<<<<<<<<<<< @@ -97406,7 +96519,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal } __pyx_L6_break:; 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__Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(2, 393, __pyx_L1_error) + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(2, 397, __pyx_L1_error) #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 393, __pyx_L1_error) + __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 397, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } else { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(2, 393, __pyx_L1_error) + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(2, 397, __pyx_L1_error) #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); 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__pyx_v_info->shape = __pyx_t_4; - /* "View.MemoryView":518 + /* "View.MemoryView":522 * raise ValueError("Cannot create writable memory view from read-only memoryview") * * if flags & PyBUF_ND: # <<<<<<<<<<<<<< @@ -99260,7 +98409,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu goto __pyx_L6; } - /* "View.MemoryView":521 + /* "View.MemoryView":525 * info.shape = self.view.shape * else: * info.shape = NULL # <<<<<<<<<<<<<< @@ -99272,7 +98421,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu } __pyx_L6:; - /* "View.MemoryView":523 + /* "View.MemoryView":527 * info.shape = NULL * * if flags & PyBUF_STRIDES: # <<<<<<<<<<<<<< @@ -99282,7 +98431,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_STRIDES) != 0); if (__pyx_t_1) { - /* "View.MemoryView":524 + /* "View.MemoryView":528 * * if flags & PyBUF_STRIDES: * info.strides = self.view.strides # <<<<<<<<<<<<<< @@ -99292,7 +98441,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_4 = __pyx_v_self->view.strides; 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- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(2, 758, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(2, 762, __pyx_L1_error) if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 758, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 762, __pyx_L1_error) __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L11_bool_binop_done; @@ -102082,55 +101304,55 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L11_bool_binop_done:; __pyx_v_step = __pyx_t_10; - /* "View.MemoryView":760 + /* "View.MemoryView":764 * step = index.step or 0 * * have_start = index.start is not None # <<<<<<<<<<<<<< * have_stop = index.stop is not None * have_step = index.step is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 760, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 764, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_start = __pyx_t_1; - /* "View.MemoryView":761 + /* "View.MemoryView":765 * * have_start = index.start is not None * have_stop = index.stop is not None # <<<<<<<<<<<<<< * have_step = index.step is not None * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 761, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 765, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_stop = __pyx_t_1; - /* "View.MemoryView":762 + /* "View.MemoryView":766 * have_start = index.start is not None * have_stop = index.stop is not None * have_step = index.step is not None # <<<<<<<<<<<<<< * * slice_memviewslice( */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 762, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 766, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_step = __pyx_t_1; - /* "View.MemoryView":764 + /* "View.MemoryView":768 * have_step = index.step is not None * * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 764, __pyx_L1_error) + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(2, 768, __pyx_L1_error) - /* "View.MemoryView":770 + /* "View.MemoryView":774 * have_start, have_stop, have_step, * True) * new_ndim += 1 # <<<<<<<<<<<<<< @@ -102141,7 +101363,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L6:; - /* "View.MemoryView":742 + /* "View.MemoryView":746 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -102151,7 +101373,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -102162,7 +101384,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< @@ -102171,39 +101393,39 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":774 + /* "View.MemoryView":778 * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, # <<<<<<<<<<<<<< * memviewsliceobj.to_dtype_func, * memview.dtype_is_object) */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 774, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 778, __pyx_L1_error) } - /* "View.MemoryView":775 + /* "View.MemoryView":779 * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, # <<<<<<<<<<<<<< * memview.dtype_is_object) * else: */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 775, __pyx_L1_error) } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); __PYX_ERR(2, 779, __pyx_L1_error) } - /* "View.MemoryView":773 + /* "View.MemoryView":777 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 773, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 777, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 773, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 777, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; - /* "View.MemoryView":772 + /* "View.MemoryView":776 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -102212,7 +101434,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ } - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< @@ -102222,30 +101444,30 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ /*else*/ { __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":779 + /* "View.MemoryView":783 * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 778, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 782, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - /* "View.MemoryView":778 + /* "View.MemoryView":782 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 778, __pyx_L1_error) + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) __PYX_ERR(2, 782, __pyx_L1_error) __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":706 + /* "View.MemoryView":710 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -102268,7 +101490,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ return __pyx_r; } -/* "View.MemoryView":803 +/* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -102284,9 +101506,12 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, int __pyx_t_1; int __pyx_t_2; int __pyx_t_3; - __Pyx_TraceCall("slice_memviewslice", __pyx_f[2], 803, 1, __PYX_ERR(2, 803, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("slice_memviewslice", __pyx_f[2], 807, 1, __PYX_ERR(2, 807, __pyx_L1_error)); - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -102296,7 +101521,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -102306,7 +101531,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((__pyx_v_start < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":826 + /* "View.MemoryView":830 * * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -102315,7 +101540,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":825 + /* "View.MemoryView":829 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -102324,7 +101549,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -102338,16 +101563,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":828 + /* "View.MemoryView":832 * start += shape * if not 0 <= start < shape: * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< * else: * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 828, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 832, __pyx_L1_error) - /* "View.MemoryView":827 + /* "View.MemoryView":831 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -102356,7 +101581,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":823 + /* "View.MemoryView":827 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -102366,7 +101591,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L3; } - /* "View.MemoryView":831 + /* "View.MemoryView":835 * else: * * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< @@ -102385,7 +101610,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L6_bool_binop_done:; __pyx_v_negative_step = __pyx_t_2; - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -102403,16 +101628,16 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L9_bool_binop_done:; if (__pyx_t_2) { - /* "View.MemoryView":834 + /* "View.MemoryView":838 * * if have_step and step == 0: * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 834, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 838, __pyx_L1_error) - /* "View.MemoryView":833 + /* "View.MemoryView":837 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -102421,7 +101646,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -102431,7 +101656,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_start != 0); if (__pyx_t_2) { - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -102441,7 +101666,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":839 + /* "View.MemoryView":843 * if have_start: * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -102450,7 +101675,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -102460,7 +101685,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":841 + /* "View.MemoryView":845 * start += shape * if start < 0: * start = 0 # <<<<<<<<<<<<<< @@ -102469,7 +101694,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = 0; - /* "View.MemoryView":840 + /* "View.MemoryView":844 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -102478,7 +101703,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":838 + /* "View.MemoryView":842 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -102488,7 +101713,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L12; } - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -102498,7 +101723,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -102508,7 +101733,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":844 + /* "View.MemoryView":848 * elif start >= shape: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -102517,7 +101742,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":843 + /* "View.MemoryView":847 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -102527,7 +101752,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L14; } - /* "View.MemoryView":846 + /* "View.MemoryView":850 * start = shape - 1 * else: * start = shape # <<<<<<<<<<<<<< @@ -102539,7 +101764,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L14:; - /* "View.MemoryView":842 + /* "View.MemoryView":846 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -102549,7 +101774,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L12:; - /* "View.MemoryView":837 + /* "View.MemoryView":841 * * * if have_start: # <<<<<<<<<<<<<< @@ -102559,7 +101784,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L11; } - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -102570,7 +101795,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":849 + /* "View.MemoryView":853 * else: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -102579,7 +101804,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_shape - 1); - /* "View.MemoryView":848 + /* "View.MemoryView":852 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -102589,7 +101814,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L15; } - /* "View.MemoryView":851 + /* "View.MemoryView":855 * start = shape - 1 * else: * start = 0 # <<<<<<<<<<<<<< @@ -102603,7 +101828,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L11:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -102613,7 +101838,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_stop != 0); if (__pyx_t_2) { - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -102623,7 +101848,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":855 + /* "View.MemoryView":859 * if have_stop: * if stop < 0: * stop += shape # <<<<<<<<<<<<<< @@ -102632,7 +101857,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -102642,7 +101867,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":857 + /* "View.MemoryView":861 * stop += shape * if stop < 0: * stop = 0 # <<<<<<<<<<<<<< @@ -102651,7 +101876,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = 0; - /* "View.MemoryView":856 + /* "View.MemoryView":860 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -102660,7 +101885,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":854 + /* "View.MemoryView":858 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -102670,7 +101895,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L17; } - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -102680,7 +101905,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":859 + /* "View.MemoryView":863 * stop = 0 * elif stop > shape: * stop = shape # <<<<<<<<<<<<<< @@ -102689,7 +101914,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = __pyx_v_shape; - /* "View.MemoryView":858 + /* "View.MemoryView":862 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -102699,7 +101924,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L17:; - /* "View.MemoryView":853 + /* "View.MemoryView":857 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -102709,7 +101934,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L16; } - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -102720,7 +101945,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":862 + /* "View.MemoryView":866 * else: * if negative_step: * stop = -1 # <<<<<<<<<<<<<< @@ -102729,7 +101954,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = -1L; - /* "View.MemoryView":861 + /* "View.MemoryView":865 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< @@ -102739,7 +101964,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L19; } - /* "View.MemoryView":864 + /* "View.MemoryView":868 * stop = -1 * else: * stop = shape # <<<<<<<<<<<<<< @@ -102753,7 +101978,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L16:; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -102763,7 +101988,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":867 + /* "View.MemoryView":871 * * if not have_step: * step = 1 # <<<<<<<<<<<<<< @@ -102772,7 +101997,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_step = 1; - /* "View.MemoryView":866 + /* "View.MemoryView":870 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -102781,7 +102006,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":871 + /* "View.MemoryView":875 * * with cython.cdivision(True): * new_shape = (stop - start) // step # <<<<<<<<<<<<<< @@ -102790,7 +102015,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -102800,7 +102025,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":874 + /* "View.MemoryView":878 * * if (stop - start) - step * new_shape: * new_shape += 1 # <<<<<<<<<<<<<< @@ -102809,7 +102034,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = (__pyx_v_new_shape + 1); - /* "View.MemoryView":873 + /* "View.MemoryView":877 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -102818,7 +102043,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -102828,7 +102053,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":877 + /* "View.MemoryView":881 * * if new_shape < 0: * new_shape = 0 # <<<<<<<<<<<<<< @@ -102837,7 +102062,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = 0; - /* "View.MemoryView":876 + /* "View.MemoryView":880 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -102846,7 +102071,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":880 + /* "View.MemoryView":884 * * * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< @@ -102855,7 +102080,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - /* "View.MemoryView":881 + /* "View.MemoryView":885 * * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< @@ -102864,7 +102089,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - /* "View.MemoryView":882 + /* "View.MemoryView":886 * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< @@ -102875,7 +102100,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L3:; - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -102885,7 +102110,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":886 + /* "View.MemoryView":890 * * if suboffset_dim[0] < 0: * dst.data += start * stride # <<<<<<<<<<<<<< @@ -102894,7 +102119,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - /* "View.MemoryView":885 + /* "View.MemoryView":889 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -102904,7 +102129,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L23; } - /* "View.MemoryView":888 + /* "View.MemoryView":892 * dst.data += start * stride * else: * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< @@ -102917,7 +102142,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L23:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -102927,7 +102152,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -102937,7 +102162,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -102947,7 +102172,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":893 + /* "View.MemoryView":897 * if not is_slice: * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< @@ -102956,7 +102181,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":892 + /* "View.MemoryView":896 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -102966,7 +102191,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L26; } - /* "View.MemoryView":895 + /* "View.MemoryView":899 * dst.data = ( dst.data)[0] + suboffset * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< @@ -102975,18 +102200,18 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ /*else*/ { - /* "View.MemoryView":896 + /* "View.MemoryView":900 * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< * else: * suboffset_dim[0] = new_ndim */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 895, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"All dimensions preceding dimension %d must be indexed and not sliced"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 899, __pyx_L1_error) } __pyx_L26:; - /* "View.MemoryView":891 + /* "View.MemoryView":895 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -102996,7 +102221,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, goto __pyx_L25; } - /* "View.MemoryView":898 + /* "View.MemoryView":902 * "must be indexed and not sliced", dim) * else: * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< @@ -103008,7 +102233,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L25:; - /* "View.MemoryView":890 + /* "View.MemoryView":894 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -103017,7 +102242,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ } - /* "View.MemoryView":900 + /* "View.MemoryView":904 * suboffset_dim[0] = new_ndim * * return 0 # <<<<<<<<<<<<<< @@ -103027,7 +102252,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":803 + /* "View.MemoryView":807 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -103052,7 +102277,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, return __pyx_r; } -/* "View.MemoryView":906 +/* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -103073,10 +102298,13 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("pybuffer_index", 0); - __Pyx_TraceCall("pybuffer_index", __pyx_f[2], 906, 0, __PYX_ERR(2, 906, __pyx_L1_error)); + __Pyx_TraceCall("pybuffer_index", __pyx_f[2], 910, 0, __PYX_ERR(2, 910, __pyx_L1_error)); - /* "View.MemoryView":908 + /* "View.MemoryView":912 * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< @@ -103085,7 +102313,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_suboffset = -1L; 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if (unlikely(__pyx_t_2)) { - /* "View.MemoryView":924 + /* "View.MemoryView":928 * index += view.shape[dim] * if index < 0: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * if index >= shape: */ - __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 928, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 928, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 924, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); 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if (unlikely(__pyx_t_2)) { - /* "View.MemoryView":927 + /* "View.MemoryView":931 * * if index >= shape: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * resultp = bufp + index * stride */ - __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 931, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 931, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 927, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_4); 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if (__pyx_t_2) { - /* "View.MemoryView":931 + /* "View.MemoryView":935 * resultp = bufp + index * stride * if suboffset >= 0: * resultp = ( resultp)[0] + suboffset # <<<<<<<<<<<<<< @@ -103322,7 +102550,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset); - /* "View.MemoryView":930 + /* "View.MemoryView":934 * * resultp = bufp + index * stride * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -103331,7 +102559,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ } - /* "View.MemoryView":933 + /* "View.MemoryView":937 * resultp = ( resultp)[0] + suboffset * * return resultp # <<<<<<<<<<<<<< @@ -103341,7 +102569,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_r = __pyx_v_resultp; goto __pyx_L0; - /* "View.MemoryView":906 + /* "View.MemoryView":910 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -103361,7 +102589,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P return __pyx_r; } -/* "View.MemoryView":939 +/* "View.MemoryView":943 * * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: # <<<<<<<<<<<<<< @@ -103386,9 +102614,12 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { int __pyx_t_7; int __pyx_t_8; int __pyx_t_9; - __Pyx_TraceCall("transpose_memslice", __pyx_f[2], 939, 1, __PYX_ERR(2, 939, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("transpose_memslice", __pyx_f[2], 943, 1, __PYX_ERR(2, 943, __pyx_L1_error)); - /* "View.MemoryView":940 + /* "View.MemoryView":944 * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: * cdef int ndim = memslice.memview.view.ndim # <<<<<<<<<<<<<< @@ -103398,7 +102629,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_1 = __pyx_v_memslice->memview->view.ndim; __pyx_v_ndim = __pyx_t_1; 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if (__pyx_t_7) { - /* "View.MemoryView":953 + /* "View.MemoryView":957 * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: * _err(ValueError, "Cannot transpose memoryview with indirect dimensions") # <<<<<<<<<<<<<< * * return 1 */ - __pyx_t_9 = __pyx_memoryview_err(__pyx_builtin_ValueError, ((char *)"Cannot transpose memoryview with indirect dimensions")); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(2, 953, __pyx_L1_error) + __pyx_t_9 = __pyx_memoryview_err(__pyx_builtin_ValueError, ((char *)"Cannot transpose memoryview with indirect dimensions")); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(2, 957, __pyx_L1_error) - /* "View.MemoryView":952 + /* "View.MemoryView":956 * shape[i], shape[j] = shape[j], shape[i] * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: # <<<<<<<<<<<<<< @@ -103500,7 +102731,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { } } - /* "View.MemoryView":955 + /* "View.MemoryView":959 * _err(ValueError, "Cannot transpose memoryview with indirect dimensions") * * return 1 # <<<<<<<<<<<<<< @@ -103510,7 +102741,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_r = 1; 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__pyx_v_result->__pyx_base.typeinfo = __pyx_t_4; - /* "View.MemoryView":1017 + /* "View.MemoryView":1021 * result.typeinfo = memviewslice.memview.typeinfo * * result.view = memviewslice.memview.view # <<<<<<<<<<<<<< @@ -104063,7 +103315,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_5 = __pyx_v_memviewslice.memview->view; __pyx_v_result->__pyx_base.view = __pyx_t_5; - /* "View.MemoryView":1018 + /* "View.MemoryView":1022 * * result.view = memviewslice.memview.view * result.view.buf = memviewslice.data # <<<<<<<<<<<<<< @@ -104072,7 +103324,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.buf = ((void *)__pyx_v_memviewslice.data); - /* "View.MemoryView":1019 + /* "View.MemoryView":1023 * result.view = memviewslice.memview.view * result.view.buf = memviewslice.data * result.view.ndim = ndim # <<<<<<<<<<<<<< @@ -104081,7 +103333,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.ndim = __pyx_v_ndim; - /* "View.MemoryView":1020 + /* "View.MemoryView":1024 * result.view.buf = memviewslice.data * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None # <<<<<<<<<<<<<< @@ -104090,7 +103342,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ ((Py_buffer *)(&__pyx_v_result->__pyx_base.view))->obj = Py_None; - /* "View.MemoryView":1021 + /* "View.MemoryView":1025 * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None * Py_INCREF(Py_None) # <<<<<<<<<<<<<< @@ -104099,7 +103351,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ Py_INCREF(Py_None); - /* "View.MemoryView":1023 + /* "View.MemoryView":1027 * Py_INCREF(Py_None) * * if (memviewslice.memview).flags & PyBUF_WRITABLE: # <<<<<<<<<<<<<< @@ -104109,7 +103361,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((((struct __pyx_memoryview_obj *)__pyx_v_memviewslice.memview)->flags & PyBUF_WRITABLE) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1024 + /* "View.MemoryView":1028 * * if (memviewslice.memview).flags & PyBUF_WRITABLE: * result.flags = PyBUF_RECORDS # <<<<<<<<<<<<<< @@ -104118,7 +103370,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.flags = PyBUF_RECORDS; - /* "View.MemoryView":1023 + /* "View.MemoryView":1027 * Py_INCREF(Py_None) * * if (memviewslice.memview).flags & PyBUF_WRITABLE: # <<<<<<<<<<<<<< @@ -104128,7 +103380,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl goto __pyx_L4; } - /* "View.MemoryView":1026 + /* "View.MemoryView":1030 * result.flags = PyBUF_RECORDS * else: * result.flags = PyBUF_RECORDS_RO # <<<<<<<<<<<<<< @@ -104140,7 +103392,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L4:; - /* "View.MemoryView":1028 + /* "View.MemoryView":1032 * result.flags = PyBUF_RECORDS_RO * * result.view.shape = result.from_slice.shape # <<<<<<<<<<<<<< @@ -104149,7 +103401,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.shape = ((Py_ssize_t *)__pyx_v_result->from_slice.shape); - /* "View.MemoryView":1029 + /* "View.MemoryView":1033 * * result.view.shape = result.from_slice.shape * result.view.strides = result.from_slice.strides # <<<<<<<<<<<<<< @@ -104158,7 +103410,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.strides = ((Py_ssize_t *)__pyx_v_result->from_slice.strides); - /* "View.MemoryView":1032 + /* "View.MemoryView":1036 * * * result.view.suboffsets = NULL # <<<<<<<<<<<<<< @@ -104167,7 +103419,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = NULL; - /* "View.MemoryView":1033 + /* "View.MemoryView":1037 * * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: # <<<<<<<<<<<<<< @@ -104179,7 +103431,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_6 = __pyx_t_8; __pyx_v_suboffset = (__pyx_t_6[0]); - /* "View.MemoryView":1034 + /* "View.MemoryView":1038 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -104189,7 +103441,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1035 + /* "View.MemoryView":1039 * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets # <<<<<<<<<<<<<< @@ -104198,7 +103450,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = ((Py_ssize_t *)__pyx_v_result->from_slice.suboffsets); - /* "View.MemoryView":1036 + /* "View.MemoryView":1040 * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets * break # <<<<<<<<<<<<<< @@ -104207,7 +103459,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ goto __pyx_L6_break; - /* "View.MemoryView":1034 + /* "View.MemoryView":1038 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -104218,7 +103470,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl } __pyx_L6_break:; 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__Pyx_XDECREF_SET(__pyx_v_length, __pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":1040 + /* "View.MemoryView":1044 * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: * result.view.len *= length # <<<<<<<<<<<<<< * * result.to_object_func = to_object_func */ - __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 1040, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 1044, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; } - /* "View.MemoryView":1042 + /* "View.MemoryView":1046 * result.view.len *= length * * result.to_object_func = to_object_func # <<<<<<<<<<<<<< @@ -104269,7 +103521,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_object_func = __pyx_v_to_object_func; - /* "View.MemoryView":1043 + /* "View.MemoryView":1047 * * result.to_object_func = to_object_func * result.to_dtype_func = to_dtype_func # <<<<<<<<<<<<<< @@ -104278,7 +103530,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_dtype_func = __pyx_v_to_dtype_func; - /* "View.MemoryView":1045 + /* "View.MemoryView":1049 * result.to_dtype_func = to_dtype_func * * return result # <<<<<<<<<<<<<< @@ -104290,7 +103542,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":995 + /* "View.MemoryView":999 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -104313,11 +103565,11 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl return __pyx_r; } -/* "View.MemoryView":1048 +/* "View.MemoryView":1052 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *mslice): + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj */ @@ -104329,11 +103581,14 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p int __pyx_t_1; int __pyx_t_2; PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_slice_from_memview", 0); - __Pyx_TraceCall("get_slice_from_memview", __pyx_f[2], 1048, 0, __PYX_ERR(2, 1048, __pyx_L1_error)); + __Pyx_TraceCall("get_slice_from_memview", __pyx_f[2], 1052, 0, __PYX_ERR(2, 1052, __pyx_L1_error)); - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -104343,20 +103598,20 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1052 + /* "View.MemoryView":1056 * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): * obj = memview # <<<<<<<<<<<<<< * return &obj.from_slice * else: */ - if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(2, 1052, __pyx_L1_error) + if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) __PYX_ERR(2, 1056, __pyx_L1_error) __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_obj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":1053 + /* "View.MemoryView":1057 * if isinstance(memview, _memoryviewslice): * obj = memview * return &obj.from_slice # <<<<<<<<<<<<<< @@ -104366,8 +103621,8 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p __pyx_r = (&__pyx_v_obj->from_slice); goto __pyx_L0; - /* "View.MemoryView":1051 - * __Pyx_memviewslice *mslice): + /* "View.MemoryView":1055 + * __Pyx_memviewslice *mslice) except NULL: * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview @@ -104375,7 +103630,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p */ } - /* "View.MemoryView":1055 + /* "View.MemoryView":1059 * return &obj.from_slice * else: * slice_copy(memview, mslice) # <<<<<<<<<<<<<< @@ -104385,7 +103640,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, __pyx_v_mslice); 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__pyx_v_strides = __pyx_t_1; - /* "View.MemoryView":1065 + /* "View.MemoryView":1069 * shape = memview.view.shape * strides = memview.view.strides * suboffsets = memview.view.suboffsets # <<<<<<<<<<<<<< @@ -104469,7 +103727,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.suboffsets; __pyx_v_suboffsets = __pyx_t_1; - /* "View.MemoryView":1067 + /* "View.MemoryView":1071 * suboffsets = memview.view.suboffsets * * dst.memview = <__pyx_memoryview *> memview # <<<<<<<<<<<<<< @@ -104478,7 +103736,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->memview = ((struct __pyx_memoryview_obj *)__pyx_v_memview); - /* "View.MemoryView":1068 + /* "View.MemoryView":1072 * * dst.memview = <__pyx_memoryview *> memview * dst.data = memview.view.buf # <<<<<<<<<<<<<< @@ -104487,7 +103745,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->data = ((char *)__pyx_v_memview->view.buf); 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- /* "View.MemoryView":1073 + /* "View.MemoryView":1077 * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 # <<<<<<<<<<<<<< @@ -104532,7 +103790,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_5; } - /* "View.MemoryView":1059 + /* "View.MemoryView":1063 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -104549,7 +103807,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1076 +/* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -104563,10 +103821,13 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy", 0); - __Pyx_TraceCall("memoryview_copy", __pyx_f[2], 1076, 0, __PYX_ERR(2, 1076, __pyx_L1_error)); + __Pyx_TraceCall("memoryview_copy", __pyx_f[2], 1080, 0, __PYX_ERR(2, 1080, __pyx_L1_error)); - /* "View.MemoryView":1079 + /* "View.MemoryView":1083 * "Create a new memoryview object" * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -104575,7 +103836,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx */ __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_memviewslice)); - /* "View.MemoryView":1080 + /* "View.MemoryView":1084 * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) * return memoryview_copy_from_slice(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -104583,13 +103844,13 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx * @cname('__pyx_memoryview_copy_object_from_slice') */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1080, __pyx_L1_error) + __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1084, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "View.MemoryView":1076 + /* "View.MemoryView":1080 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -104609,7 +103870,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx return __pyx_r; } -/* "View.MemoryView":1083 +/* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -104628,10 +103889,13 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview PyObject *(*__pyx_t_3)(char *); int (*__pyx_t_4)(char *, PyObject *); PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy_from_slice", 0); - __Pyx_TraceCall("memoryview_copy_from_slice", __pyx_f[2], 1083, 0, __PYX_ERR(2, 1083, __pyx_L1_error)); + __Pyx_TraceCall("memoryview_copy_from_slice", __pyx_f[2], 1087, 0, __PYX_ERR(2, 1087, __pyx_L1_error)); - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -104642,7 +103906,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1091 + /* "View.MemoryView":1095 * * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func # <<<<<<<<<<<<<< @@ -104652,7 +103916,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; __pyx_v_to_object_func = __pyx_t_3; - /* "View.MemoryView":1092 + /* "View.MemoryView":1096 * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< @@ -104662,7 +103926,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; __pyx_v_to_dtype_func = __pyx_t_4; - /* "View.MemoryView":1090 + /* "View.MemoryView":1094 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< @@ -104672,7 +103936,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview goto __pyx_L3; } - /* "View.MemoryView":1094 + /* "View.MemoryView":1098 * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func * else: * to_object_func = NULL # <<<<<<<<<<<<<< @@ -104682,7 +103946,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview /*else*/ { __pyx_v_to_object_func = NULL; - /* "View.MemoryView":1095 + /* "View.MemoryView":1099 * else: * to_object_func = NULL * to_dtype_func = NULL # <<<<<<<<<<<<<< @@ -104693,7 +103957,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview } __pyx_L3:; - /* "View.MemoryView":1097 + /* "View.MemoryView":1101 * to_dtype_func = NULL * * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< @@ -104702,20 +103966,20 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __Pyx_XDECREF(__pyx_r); - /* "View.MemoryView":1099 + /* "View.MemoryView":1103 * return memoryview_fromslice(memviewslice[0], memview.view.ndim, * to_object_func, to_dtype_func, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 1097, __pyx_L1_error) + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 1101, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":1083 + /* "View.MemoryView":1087 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -104735,7 +103999,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview return __pyx_r; } -/* "View.MemoryView":1105 +/* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -104747,9 +104011,12 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { Py_ssize_t __pyx_r; __Pyx_TraceDeclarations int __pyx_t_1; - __Pyx_TraceCall("abs_py_ssize_t", __pyx_f[2], 1105, 1, __PYX_ERR(2, 1105, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("abs_py_ssize_t", __pyx_f[2], 1109, 1, __PYX_ERR(2, 1109, __pyx_L1_error)); - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -104759,7 +104026,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_t_1 = ((__pyx_v_arg < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1107 + /* "View.MemoryView":1111 * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: * return -arg # <<<<<<<<<<<<<< @@ -104769,7 +104036,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_r = (-__pyx_v_arg); goto __pyx_L0; - /* "View.MemoryView":1106 + /* "View.MemoryView":1110 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -104778,7 +104045,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { */ } - /* "View.MemoryView":1109 + /* "View.MemoryView":1113 * return -arg * else: * return arg # <<<<<<<<<<<<<< @@ -104790,7 +104057,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { goto __pyx_L0; } - /* "View.MemoryView":1105 + /* "View.MemoryView":1109 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -104807,7 +104074,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { return __pyx_r; } -/* "View.MemoryView":1112 +/* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -104825,9 +104092,12 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; - __Pyx_TraceCall("get_best_order", __pyx_f[2], 1112, 1, __PYX_ERR(2, 1112, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("get_best_order", __pyx_f[2], 1116, 1, __PYX_ERR(2, 1116, __pyx_L1_error)); - /* "View.MemoryView":1117 + /* "View.MemoryView":1121 * """ * cdef int i * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< @@ -104836,7 +104106,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = 0; - /* "View.MemoryView":1118 + /* "View.MemoryView":1122 * cdef int i * cdef Py_ssize_t c_stride = 0 * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< @@ -104845,7 +104115,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = 0; - /* "View.MemoryView":1120 + /* "View.MemoryView":1124 * cdef Py_ssize_t f_stride = 0 * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -104855,7 +104125,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -104865,7 +104135,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1122 + /* "View.MemoryView":1126 * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -104874,7 +104144,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1123 + /* "View.MemoryView":1127 * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -104883,7 +104153,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L4_break; - /* "View.MemoryView":1121 + /* "View.MemoryView":1125 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -104894,7 +104164,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L4_break:; - /* "View.MemoryView":1125 + /* "View.MemoryView":1129 * break * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -104906,7 +104176,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -104916,7 +104186,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1127 + /* "View.MemoryView":1131 * for i in range(ndim): * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -104925,7 +104195,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1128 + /* "View.MemoryView":1132 * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -104934,7 +104204,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ goto __pyx_L7_break; - /* "View.MemoryView":1126 + /* "View.MemoryView":1130 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -104945,7 +104215,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ } __pyx_L7_break:; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -104955,7 +104225,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1131 + /* "View.MemoryView":1135 * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): * return 'C' # <<<<<<<<<<<<<< @@ -104965,7 +104235,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_r = 'C'; goto __pyx_L0; - /* "View.MemoryView":1130 + /* "View.MemoryView":1134 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -104974,7 +104244,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ } - /* "View.MemoryView":1133 + /* "View.MemoryView":1137 * return 'C' * else: * return 'F' # <<<<<<<<<<<<<< @@ -104986,7 +104256,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ goto __pyx_L0; } - /* "View.MemoryView":1112 + /* "View.MemoryView":1116 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -105003,7 +104273,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ return __pyx_r; } -/* "View.MemoryView":1136 +/* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -105024,7 +104294,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v Py_ssize_t __pyx_t_5; Py_ssize_t __pyx_t_6; - /* "View.MemoryView":1143 + /* "View.MemoryView":1147 * * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< @@ -105033,7 +104303,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_extent = (__pyx_v_src_shape[0]); - /* "View.MemoryView":1144 + /* "View.MemoryView":1148 * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< @@ -105042,7 +104312,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - /* "View.MemoryView":1145 + /* "View.MemoryView":1149 * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< @@ -105051,7 +104321,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_stride = (__pyx_v_src_strides[0]); - /* "View.MemoryView":1146 + /* "View.MemoryView":1150 * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< @@ -105060,7 +104330,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -105070,7 +104340,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -105090,7 +104360,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L5_bool_binop_done; } - /* "View.MemoryView":1150 + /* "View.MemoryView":1154 * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< @@ -105105,7 +104375,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = __pyx_t_3; __pyx_L5_bool_binop_done:; - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -105114,7 +104384,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ if (__pyx_t_1) { - /* "View.MemoryView":1151 + /* "View.MemoryView":1155 * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< @@ -105123,7 +104393,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - /* "View.MemoryView":1149 + /* "View.MemoryView":1153 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -105133,7 +104403,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L4; } - /* "View.MemoryView":1153 + /* "View.MemoryView":1157 * memcpy(dst_data, src_data, itemsize * dst_extent) * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -105146,7 +104416,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1154 + /* "View.MemoryView":1158 * else: * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< @@ -105155,7 +104425,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - /* "View.MemoryView":1155 + /* "View.MemoryView":1159 * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -105164,7 +104434,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1156 + /* "View.MemoryView":1160 * memcpy(dst_data, src_data, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -105176,7 +104446,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L4:; - /* "View.MemoryView":1148 + /* "View.MemoryView":1152 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -105186,7 +104456,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L3; } - /* "View.MemoryView":1158 + /* "View.MemoryView":1162 * dst_data += dst_stride * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< @@ -105199,7 +104469,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1159 + /* "View.MemoryView":1163 * else: * for i in range(dst_extent): * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< @@ -105208,7 +104478,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - /* "View.MemoryView":1163 + /* "View.MemoryView":1167 * src_shape + 1, dst_shape + 1, * ndim - 1, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -105217,7 +104487,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1164 + /* "View.MemoryView":1168 * ndim - 1, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -105229,7 +104499,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L3:; - /* "View.MemoryView":1136 + /* "View.MemoryView":1140 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -105240,7 +104510,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v /* function exit code */ } -/* "View.MemoryView":1166 +/* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -105250,9 +104520,12 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { __Pyx_TraceDeclarations - __Pyx_TraceCall("copy_strided_to_strided", __pyx_f[2], 1166, 1, __PYX_ERR(2, 1166, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("copy_strided_to_strided", __pyx_f[2], 1170, 1, __PYX_ERR(2, 1170, __pyx_L1_error)); - /* "View.MemoryView":1169 + /* "View.MemoryView":1173 * __Pyx_memviewslice *dst, * int ndim, size_t itemsize) nogil: * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< @@ -105261,7 +104534,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi */ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1166 + /* "View.MemoryView":1170 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -105277,59 +104550,62 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi __Pyx_TraceReturn(Py_None, 1); } -/* "View.MemoryView":1173 +/* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - int __pyx_v_i; + Py_ssize_t __pyx_v_shape; Py_ssize_t __pyx_v_size; Py_ssize_t __pyx_r; __Pyx_TraceDeclarations Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - __Pyx_TraceCall("slice_get_size", __pyx_f[2], 1173, 1, __PYX_ERR(2, 1173, __pyx_L1_error)); + Py_ssize_t *__pyx_t_2; + Py_ssize_t *__pyx_t_3; + Py_ssize_t *__pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("slice_get_size", __pyx_f[2], 1177, 1, __PYX_ERR(2, 1177, __pyx_L1_error)); - /* "View.MemoryView":1176 + /* "View.MemoryView":1179 + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< * - * for i in range(ndim): + * for shape in src.shape[:ndim]: */ __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_size = __pyx_t_1; - /* "View.MemoryView":1178 - * cdef Py_ssize_t size = src.memview.view.itemsize + /* "View.MemoryView":1181 + * cdef Py_ssize_t shape, size = src.memview.view.itemsize * - * for i in range(ndim): # <<<<<<<<<<<<<< - * size *= src.shape[i] + * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< + * size *= shape * */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; + __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); + for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { + __pyx_t_2 = __pyx_t_4; + __pyx_v_shape = (__pyx_t_2[0]); - /* "View.MemoryView":1179 + /* "View.MemoryView":1182 * - * for i in range(ndim): - * size *= src.shape[i] # <<<<<<<<<<<<<< + * for shape in src.shape[:ndim]: + * size *= shape # <<<<<<<<<<<<<< * * return size */ - __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + __pyx_v_size = (__pyx_v_size * __pyx_v_shape); } - /* "View.MemoryView":1181 - * size *= src.shape[i] + /* "View.MemoryView":1184 + * size *= shape * * return size # <<<<<<<<<<<<<< * @@ -105338,12 +104614,12 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_r = __pyx_v_size; goto __pyx_L0; - /* "View.MemoryView":1173 + /* "View.MemoryView":1177 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i + * cdef Py_ssize_t shape, size = src.memview.view.itemsize */ /* function exit code */ @@ -105355,7 +104631,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr return __pyx_r; } -/* "View.MemoryView":1184 +/* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -105371,9 +104647,12 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; - __Pyx_TraceCall("fill_contig_strides_array", __pyx_f[2], 1184, 1, __PYX_ERR(2, 1184, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("fill_contig_strides_array", __pyx_f[2], 1187, 1, __PYX_ERR(2, 1187, __pyx_L1_error)); - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -105383,38 +104662,38 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_t_1 = ((__pyx_v_order == 'F') != 0); if (__pyx_t_1) { - /* "View.MemoryView":1194 + /* "View.MemoryView":1197 * * if order == 'F': * for idx in range(ndim): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ __pyx_t_2 = __pyx_v_ndim; __pyx_t_3 = __pyx_t_2; for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_idx = __pyx_t_4; - /* "View.MemoryView":1195 + /* "View.MemoryView":1198 * if order == 'F': * for idx in range(ndim): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * else: */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1196 + /* "View.MemoryView":1199 * for idx in range(ndim): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * else: * for idx in range(ndim - 1, -1, -1): */ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); } - /* "View.MemoryView":1193 + /* "View.MemoryView":1196 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -105424,30 +104703,30 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ goto __pyx_L3; } - /* "View.MemoryView":1198 - * stride = stride * shape[idx] + /* "View.MemoryView":1201 + * stride *= shape[idx] * else: * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * strides[idx] = stride - * stride = stride * shape[idx] + * stride *= shape[idx] */ /*else*/ { for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; - /* "View.MemoryView":1199 + /* "View.MemoryView":1202 * else: * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] + * stride *= shape[idx] * */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1200 + /* "View.MemoryView":1203 * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * stride *= shape[idx] # <<<<<<<<<<<<<< * * return stride */ @@ -105456,8 +104735,8 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ } __pyx_L3:; - /* "View.MemoryView":1202 - * stride = stride * shape[idx] + /* "View.MemoryView":1205 + * stride *= shape[idx] * * return stride # <<<<<<<<<<<<<< * @@ -105466,7 +104745,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_r = __pyx_v_stride; goto __pyx_L0; - /* "View.MemoryView":1184 + /* "View.MemoryView":1187 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -105483,7 +104762,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ return __pyx_r; } -/* "View.MemoryView":1205 +/* "View.MemoryView":1208 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -105504,9 +104783,12 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, struct __pyx_memoryview_obj *__pyx_t_4; int __pyx_t_5; int __pyx_t_6; - __Pyx_TraceCall("copy_data_to_temp", __pyx_f[2], 1205, 1, __PYX_ERR(2, 1205, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("copy_data_to_temp", __pyx_f[2], 1208, 1, __PYX_ERR(2, 1208, __pyx_L1_error)); - /* "View.MemoryView":1216 + /* "View.MemoryView":1219 * cdef void *result * * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -105516,7 +104798,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1217 + /* "View.MemoryView":1220 * * cdef size_t itemsize = src.memview.view.itemsize * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< @@ -105525,7 +104807,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - /* "View.MemoryView":1219 + /* "View.MemoryView":1222 * cdef size_t size = slice_get_size(src, ndim) * * result = malloc(size) # <<<<<<<<<<<<<< @@ -105534,7 +104816,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_result = malloc(__pyx_v_size); - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -105544,16 +104826,16 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1221 + /* "View.MemoryView":1224 * result = malloc(size) * if not result: * _err(MemoryError, NULL) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1221, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1224, __pyx_L1_error) - /* "View.MemoryView":1220 + /* "View.MemoryView":1223 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -105562,7 +104844,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ } - /* "View.MemoryView":1224 + /* "View.MemoryView":1227 * * * tmpslice.data = result # <<<<<<<<<<<<<< @@ -105571,7 +104853,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - /* "View.MemoryView":1225 + /* "View.MemoryView":1228 * * tmpslice.data = result * tmpslice.memview = src.memview # <<<<<<<<<<<<<< @@ -105581,7 +104863,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_4 = __pyx_v_src->memview; __pyx_v_tmpslice->memview = __pyx_t_4; - /* "View.MemoryView":1226 + /* "View.MemoryView":1229 * tmpslice.data = result * tmpslice.memview = src.memview * for i in range(ndim): # <<<<<<<<<<<<<< @@ -105593,7 +104875,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "View.MemoryView":1227 + /* "View.MemoryView":1230 * tmpslice.memview = src.memview * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< @@ -105602,7 +104884,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - /* "View.MemoryView":1228 + /* "View.MemoryView":1231 * for i in range(ndim): * tmpslice.shape[i] = src.shape[i] * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -105612,7 +104894,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1230 + /* "View.MemoryView":1233 * tmpslice.suboffsets[i] = -1 * * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< @@ -105621,7 +104903,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - /* "View.MemoryView":1234 + /* "View.MemoryView":1237 * * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -105633,7 +104915,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; 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- __PYX_ERR(2, 1262, __pyx_L1_error) + __PYX_ERR(2, 1265, __pyx_L1_error) } - /* "View.MemoryView":1258 + /* "View.MemoryView":1261 * * @cname('__pyx_memoryview_err') * cdef int _err(object error, char *msg) except -1 with gil: # <<<<<<<<<<<<<< @@ -106020,7 +105311,7 @@ static int __pyx_memoryview_err(PyObject *__pyx_v_error, char *__pyx_v_msg) { return __pyx_r; } -/* "View.MemoryView":1265 +/* "View.MemoryView":1268 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -106047,9 +105338,12 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ int __pyx_t_6; void *__pyx_t_7; int __pyx_t_8; - __Pyx_TraceCall("memoryview_copy_contents", __pyx_f[2], 1265, 1, __PYX_ERR(2, 1265, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("memoryview_copy_contents", __pyx_f[2], 1268, 1, __PYX_ERR(2, 1268, __pyx_L1_error)); - /* "View.MemoryView":1273 + /* "View.MemoryView":1276 * Check for overlapping memory and verify the shapes. * """ * cdef void *tmpdata = NULL # <<<<<<<<<<<<<< @@ -106058,7 +105352,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_tmpdata = NULL; 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- /* "View.MemoryView":1278 + /* "View.MemoryView":1281 * cdef char order = get_best_order(&src, src_ndim) * cdef bint broadcasting = False * cdef bint direct_copy = False # <<<<<<<<<<<<<< @@ -106095,7 +105389,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = 0; - /* "View.MemoryView":1281 + /* "View.MemoryView":1284 * cdef __Pyx_memviewslice tmp * * if src_ndim < dst_ndim: # <<<<<<<<<<<<<< @@ -106105,7 +105399,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((__pyx_v_src_ndim < __pyx_v_dst_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1282 + /* "View.MemoryView":1285 * * if src_ndim < dst_ndim: * broadcast_leading(&src, src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -106114,7 +105408,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_broadcast_leading((&__pyx_v_src), __pyx_v_src_ndim, __pyx_v_dst_ndim); - /* "View.MemoryView":1281 + /* "View.MemoryView":1284 * cdef __Pyx_memviewslice tmp * * if src_ndim < dst_ndim: # <<<<<<<<<<<<<< @@ -106124,7 +105418,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L3; } - /* "View.MemoryView":1283 + /* "View.MemoryView":1286 * if src_ndim < dst_ndim: * broadcast_leading(&src, src_ndim, dst_ndim) * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< @@ -106134,7 +105428,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((__pyx_v_dst_ndim < __pyx_v_src_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1284 + /* "View.MemoryView":1287 * broadcast_leading(&src, src_ndim, dst_ndim) * elif dst_ndim < src_ndim: * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<< @@ -106143,7 +105437,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim); - /* "View.MemoryView":1283 + /* "View.MemoryView":1286 * if src_ndim < dst_ndim: * broadcast_leading(&src, src_ndim, dst_ndim) * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< @@ -106153,7 +105447,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_L3:; - /* "View.MemoryView":1286 + /* "View.MemoryView":1289 * broadcast_leading(&dst, dst_ndim, src_ndim) * * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -106169,7 +105463,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_v_ndim = __pyx_t_5; - /* "View.MemoryView":1288 + /* "View.MemoryView":1291 * cdef int ndim = max(src_ndim, dst_ndim) * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -106181,7 +105475,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -106191,7 +105485,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -106201,7 +105495,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1291 + /* "View.MemoryView":1294 * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: * broadcasting = True # <<<<<<<<<<<<<< @@ -106210,7 +105504,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 1; - /* "View.MemoryView":1292 + /* "View.MemoryView":1295 * if src.shape[i] == 1: * broadcasting = True * src.strides[i] = 0 # <<<<<<<<<<<<<< @@ -106219,7 +105513,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (__pyx_v_src.strides[__pyx_v_i]) = 0; - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -106229,7 +105523,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L7; } - /* "View.MemoryView":1294 + /* "View.MemoryView":1297 * src.strides[i] = 0 * else: * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< @@ -106237,11 +105531,11 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if src.suboffsets[i] >= 0: */ /*else*/ { - __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1294, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1297, __pyx_L1_error) } __pyx_L7:; - /* "View.MemoryView":1289 + /* "View.MemoryView":1292 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -106250,7 +105544,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -106260,16 +105554,16 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1297 + /* "View.MemoryView":1300 * * if src.suboffsets[i] >= 0: * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< * * if slices_overlap(&src, &dst, ndim, itemsize): */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1297, __pyx_L1_error) + __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1300, __pyx_L1_error) - /* "View.MemoryView":1296 + /* "View.MemoryView":1299 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -106279,7 +105573,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } } - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -106289,7 +105583,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -106299,7 +105593,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1302 + /* "View.MemoryView":1305 * * if not slice_is_contig(src, order, ndim): * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< @@ -106308,7 +105602,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< @@ -106317,17 +105611,17 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1304 + /* "View.MemoryView":1307 * order = get_best_order(&dst, ndim) * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< * src = tmp * */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1304, __pyx_L1_error) + __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1307, __pyx_L1_error) __pyx_v_tmpdata = __pyx_t_7; - /* "View.MemoryView":1305 + /* "View.MemoryView":1308 * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) * src = tmp # <<<<<<<<<<<<<< @@ -106336,7 +105630,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_src = __pyx_v_tmp; - /* "View.MemoryView":1299 + /* "View.MemoryView":1302 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -106345,7 +105639,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -106355,7 +105649,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -106365,7 +105659,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1311 + /* "View.MemoryView":1314 * * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< @@ -106374,7 +105668,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - /* "View.MemoryView":1310 + /* "View.MemoryView":1313 * * * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< @@ -106384,7 +105678,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ goto __pyx_L12; } - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -106394,7 +105688,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1313 + /* "View.MemoryView":1316 * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< @@ -106403,7 +105697,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - /* "View.MemoryView":1312 + /* "View.MemoryView":1315 * if slice_is_contig(src, 'C', ndim): * direct_copy = slice_is_contig(dst, 'C', ndim) * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< @@ -106413,7 +105707,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_L12:; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -106423,7 +105717,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_v_direct_copy != 0); if (__pyx_t_2) { - /* "View.MemoryView":1317 + /* "View.MemoryView":1320 * if direct_copy: * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -106432,7 +105726,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1318 + /* "View.MemoryView":1321 * * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< @@ -106441,7 +105735,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - /* "View.MemoryView":1319 + /* "View.MemoryView":1322 * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -106450,7 +105744,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1320 + /* "View.MemoryView":1323 * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) # <<<<<<<<<<<<<< @@ -106459,7 +105753,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1321 + /* "View.MemoryView":1324 * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -106469,7 +105763,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1315 + /* "View.MemoryView":1318 * direct_copy = slice_is_contig(dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -106478,7 +105772,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -106487,7 +105781,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -106501,25 +105795,25 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_8 = (__pyx_t_2 != 0); if (__pyx_t_8) { - /* "View.MemoryView":1326 + /* "View.MemoryView":1329 * * * transpose_memslice(&src) # <<<<<<<<<<<<<< * transpose_memslice(&dst) * */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1326, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1329, __pyx_L1_error) - /* "View.MemoryView":1327 + /* "View.MemoryView":1330 * * transpose_memslice(&src) * transpose_memslice(&dst) # <<<<<<<<<<<<<< * * refcount_copying(&dst, dtype_is_object, ndim, False) */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1327, __pyx_L1_error) + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1330, __pyx_L1_error) - /* "View.MemoryView":1323 + /* "View.MemoryView":1326 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -106528,7 +105822,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ } - /* "View.MemoryView":1329 + /* "View.MemoryView":1332 * transpose_memslice(&dst) * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -106537,7 +105831,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1330 + /* "View.MemoryView":1333 * * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< @@ -106546,7 +105840,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1331 + /* "View.MemoryView":1334 * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -106555,7 +105849,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1333 + /* "View.MemoryView":1336 * refcount_copying(&dst, dtype_is_object, ndim, True) * * free(tmpdata) # <<<<<<<<<<<<<< @@ -106564,7 +105858,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1334 + /* "View.MemoryView":1337 * * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -106574,7 +105868,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1265 + /* "View.MemoryView":1268 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -106599,7 +105893,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ return __pyx_r; } -/* "View.MemoryView":1337 +/* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -106614,9 +105908,12 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic int __pyx_t_1; int __pyx_t_2; int __pyx_t_3; - __Pyx_TraceCall("broadcast_leading", __pyx_f[2], 1337, 1, __PYX_ERR(2, 1337, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("broadcast_leading", __pyx_f[2], 1340, 1, __PYX_ERR(2, 1340, __pyx_L1_error)); - /* "View.MemoryView":1341 + /* "View.MemoryView":1344 * int ndim_other) nogil: * cdef int i * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< @@ -106625,7 +105922,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); - /* "View.MemoryView":1343 + /* "View.MemoryView":1346 * cdef int offset = ndim_other - ndim * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -106635,7 +105932,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1344 + /* "View.MemoryView":1347 * * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< @@ -106644,7 +105941,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); - /* "View.MemoryView":1345 + /* "View.MemoryView":1348 * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< @@ -106653,7 +105950,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1346 + /* "View.MemoryView":1349 * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< @@ -106663,7 +105960,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); } - /* "View.MemoryView":1348 + /* "View.MemoryView":1351 * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * * for i in range(offset): # <<<<<<<<<<<<<< @@ -106675,7 +105972,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1349 + /* "View.MemoryView":1352 * * for i in range(offset): * mslice.shape[i] = 1 # <<<<<<<<<<<<<< @@ -106684,7 +105981,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[__pyx_v_i]) = 1; - /* "View.MemoryView":1350 + /* "View.MemoryView":1353 * for i in range(offset): * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< @@ -106693,7 +105990,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); - /* "View.MemoryView":1351 + /* "View.MemoryView":1354 * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] * mslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< @@ -106703,7 +106000,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1337 + /* "View.MemoryView":1340 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -106719,7 +106016,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic __Pyx_TraceReturn(Py_None, 1); } -/* "View.MemoryView":1359 +/* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -106730,9 +106027,12 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { __Pyx_TraceDeclarations int __pyx_t_1; - __Pyx_TraceCall("refcount_copying", __pyx_f[2], 1359, 1, __PYX_ERR(2, 1359, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("refcount_copying", __pyx_f[2], 1362, 1, __PYX_ERR(2, 1362, __pyx_L1_error)); - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -106742,7 +106042,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __pyx_t_1 = (__pyx_v_dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":1364 + /* "View.MemoryView":1367 * * if dtype_is_object: * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< @@ -106751,7 +106051,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1363 + /* "View.MemoryView":1366 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -106760,7 +106060,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i */ } - /* "View.MemoryView":1359 + /* "View.MemoryView":1362 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -106776,7 +106076,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __Pyx_TraceReturn(Py_None, 1); } -/* "View.MemoryView":1368 +/* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -106787,13 +106087,16 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_data, Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) { __Pyx_TraceDeclarations __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; #ifdef WITH_THREAD PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure(); #endif __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0); - __Pyx_TraceCall("refcount_objects_in_slice_with_gil", __pyx_f[2], 1368, 0, __PYX_ERR(2, 1368, __pyx_L1_error)); + __Pyx_TraceCall("refcount_objects_in_slice_with_gil", __pyx_f[2], 1371, 0, __PYX_ERR(2, 1371, __pyx_L1_error)); - /* "View.MemoryView":1371 + /* "View.MemoryView":1374 * Py_ssize_t *strides, int ndim, * bint inc) with gil: * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<< @@ -106802,7 +106105,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1368 + /* "View.MemoryView":1371 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -106822,7 +106125,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif } -/* "View.MemoryView":1374 +/* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -106838,10 +106141,13 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss Py_ssize_t __pyx_t_2; Py_ssize_t __pyx_t_3; int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); - __Pyx_TraceCall("refcount_objects_in_slice", __pyx_f[2], 1374, 0, __PYX_ERR(2, 1374, __pyx_L1_error)); + __Pyx_TraceCall("refcount_objects_in_slice", __pyx_f[2], 1377, 0, __PYX_ERR(2, 1377, __pyx_L1_error)); - /* "View.MemoryView":1378 + /* "View.MemoryView":1381 * cdef Py_ssize_t i * * for i in range(shape[0]): # <<<<<<<<<<<<<< @@ -106853,7 +106159,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -106863,7 +106169,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_4) { - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -106873,7 +106179,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_4 = (__pyx_v_inc != 0); if (__pyx_t_4) { - /* "View.MemoryView":1381 + /* "View.MemoryView":1384 * if ndim == 1: * if inc: * Py_INCREF(( data)[0]) # <<<<<<<<<<<<<< @@ -106882,7 +106188,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ Py_INCREF((((PyObject **)__pyx_v_data)[0])); - /* "View.MemoryView":1380 + /* "View.MemoryView":1383 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -106892,7 +106198,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L6; } - /* "View.MemoryView":1383 + /* "View.MemoryView":1386 * Py_INCREF(( data)[0]) * else: * Py_DECREF(( data)[0]) # <<<<<<<<<<<<<< @@ -106904,7 +106210,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L6:; - /* "View.MemoryView":1379 + /* "View.MemoryView":1382 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -106914,7 +106220,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss goto __pyx_L5; } - /* "View.MemoryView":1385 + /* "View.MemoryView":1388 * Py_DECREF(( data)[0]) * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -106923,7 +106229,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss */ /*else*/ { - /* "View.MemoryView":1386 + /* "View.MemoryView":1389 * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, * ndim - 1, inc) # <<<<<<<<<<<<<< @@ -106934,7 +106240,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss } __pyx_L5:; - /* "View.MemoryView":1388 + /* "View.MemoryView":1391 * ndim - 1, inc) * * data += strides[0] # <<<<<<<<<<<<<< @@ -106944,7 +106250,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_v_data = (__pyx_v_data + (__pyx_v_strides[0])); } - /* "View.MemoryView":1374 + /* "View.MemoryView":1377 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -106961,7 +106267,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1394 +/* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -106971,9 +106277,12 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item, int __pyx_v_dtype_is_object) { __Pyx_TraceDeclarations - __Pyx_TraceCall("slice_assign_scalar", __pyx_f[2], 1394, 1, __PYX_ERR(2, 1394, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("slice_assign_scalar", __pyx_f[2], 1397, 1, __PYX_ERR(2, 1397, __pyx_L1_error)); - /* "View.MemoryView":1397 + /* "View.MemoryView":1400 * size_t itemsize, void *item, * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -106982,7 +106291,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1398 + /* "View.MemoryView":1401 * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< @@ -106991,7 +106300,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1400 + /* "View.MemoryView":1403 * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, * itemsize, item) * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -107000,7 +106309,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1394 + /* "View.MemoryView":1397 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -107016,7 +106325,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst __Pyx_TraceReturn(Py_None, 1); } -/* "View.MemoryView":1404 +/* "View.MemoryView":1407 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -107033,9 +106342,12 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t Py_ssize_t __pyx_t_2; Py_ssize_t __pyx_t_3; Py_ssize_t __pyx_t_4; - __Pyx_TraceCall("_slice_assign_scalar", __pyx_f[2], 1404, 1, __PYX_ERR(2, 1404, __pyx_L1_error)); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("_slice_assign_scalar", __pyx_f[2], 1407, 1, __PYX_ERR(2, 1407, __pyx_L1_error)); - /* "View.MemoryView":1408 + /* "View.MemoryView":1411 * size_t itemsize, void *item) nogil: * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] # <<<<<<<<<<<<<< @@ -107044,7 +106356,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_stride = (__pyx_v_strides[0]); - /* "View.MemoryView":1409 + /* "View.MemoryView":1412 * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] * cdef Py_ssize_t extent = shape[0] # <<<<<<<<<<<<<< @@ -107053,7 +106365,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_extent = (__pyx_v_shape[0]); 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N.B., `h` must be * already sorted by prefix. */ - __pyx_tuple__53 = PyTuple_Pack(16, __pyx_n_s_h, __pyx_n_s_h, __pyx_n_s_n_variants, __pyx_n_s_n_haplotypes, __pyx_n_s_pp_start, __pyx_n_s_pp_stop, __pyx_n_s_pp_size, __pyx_n_s_n0, __pyx_n_s_n1, __pyx_n_s_pp_color, __pyx_n_s_next_color, __pyx_n_s_painting, __pyx_n_s_s, __pyx_n_s_prefixes, __pyx_n_s_i, __pyx_n_s_parent_prefixes); if (unlikely(!__pyx_tuple__53)) __PYX_ERR(0, 356, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__53); - __Pyx_GIVEREF(__pyx_tuple__53); - __pyx_codeobj__54 = (PyObject*)__Pyx_PyCode_New(1, 0, 16, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__53, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_allel_opt_stats_pyx, __pyx_n_s_paint_shared_prefixes, 356, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__54)) __PYX_ERR(0, 356, __pyx_L1_error) + __pyx_tuple__51 = PyTuple_Pack(16, __pyx_n_s_h, __pyx_n_s_h, __pyx_n_s_n_variants, __pyx_n_s_n_haplotypes, __pyx_n_s_pp_start, __pyx_n_s_pp_stop, __pyx_n_s_pp_size, __pyx_n_s_n0, __pyx_n_s_n1, __pyx_n_s_pp_color, __pyx_n_s_next_color, __pyx_n_s_painting, __pyx_n_s_s, __pyx_n_s_prefixes, __pyx_n_s_i, __pyx_n_s_parent_prefixes); 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@@ -111149,7 +110489,7 @@ static int __Pyx_ParseOptionalKeywords( } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + if (likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { @@ -111176,7 +110516,7 @@ static int __Pyx_ParseOptionalKeywords( while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -111192,7 +110532,7 @@ static int __Pyx_ParseOptionalKeywords( while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; @@ -111245,7 +110585,7 @@ __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, int i, retval=-1; Py_buffer *buf = &memview->view; __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (memviewslice->memview || memviewslice->data) { + if (unlikely(memviewslice->memview || memviewslice->data)) { PyErr_SetString(PyExc_ValueError, "memviewslice is already initialized!"); goto fail; @@ -111324,13 +110664,13 @@ __Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int first_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview || (PyObject *) memview == Py_None) + if (unlikely(!memview || (PyObject *) memview == Py_None)) return; - if (__pyx_get_slice_count(memview) < 0) + if (unlikely(__pyx_get_slice_count(memview) < 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); first_time = __pyx_add_acquisition_count(memview) == 0; - if (first_time) { + if (unlikely(first_time)) { if (have_gil) { Py_INCREF((PyObject *) memview); } else { @@ -111344,18 +110684,16 @@ static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) { int last_time; struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview ) { - return; - } else if ((PyObject *) memview == Py_None) { + if (unlikely(!memview || (PyObject *) memview == Py_None)) { memslice->memview = NULL; return; } - if (__pyx_get_slice_count(memview) <= 0) + if (unlikely(__pyx_get_slice_count(memview) <= 0)) __pyx_fatalerror("Acquisition count is %d (line %d)", __pyx_get_slice_count(memview), lineno); last_time = __pyx_sub_acquisition_count(memview) == 1; memslice->data = NULL; - if (last_time) { + if (unlikely(last_time)) { if (have_gil) { Py_CLEAR(memslice->memview); } else { @@ -111460,7 +110798,7 @@ static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args return result; } #if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); PyObject *globals = PyFunction_GET_GLOBALS(func); PyObject *argdefs = PyFunction_GET_DEFAULTS(func); @@ -111531,12 +110869,12 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, } #if PY_MAJOR_VERSION >= 3 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, kwdefs, closure); #else result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, nargs, + args, (int)nargs, k, (int)nk, d, (int)nd, closure); #endif @@ -112974,9 +112312,9 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( if (stop < 0) stop += length; } - length = stop - start; - if (unlikely(length <= 0)) + if (unlikely(stop <= start)) return PyUnicode_FromUnicode(NULL, 0); + length = stop - start; cstring += start; if (decode_func) { return decode_func(cstring, length, errors); @@ -113065,7 +112403,7 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { { #if PY_MAJOR_VERSION >= 3 if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { + if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); if (!module) { @@ -113308,6 +112646,28 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable) { return -1; } +/* PyObjectGetAttrStrNoError */ +static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + __Pyx_PyErr_Clear(); +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { + return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); + } +#endif + result = __Pyx_PyObject_GetAttrStr(obj, attr_name); + if (unlikely(!result)) { + __Pyx_PyObject_GetAttrStr_ClearAttributeError(); + } + return result; +} + /* SetupReduce */ static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { int ret; @@ -113335,43 +112695,51 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { PyObject *setstate = NULL; PyObject *setstate_cython = NULL; #if CYTHON_USE_PYTYPE_LOOKUP - if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #else - if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #endif #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; if (reduce_ex == object_reduce_ex) { #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); + if (likely(reduce_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (reduce == object_reduce || PyErr_Occurred()) { + goto __PYX_BAD; + } setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); if (!setstate) PyErr_Clear(); if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); + if (likely(setstate_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (!setstate || PyErr_Occurred()) { + goto __PYX_BAD; + } } PyType_Modified((PyTypeObject*)type_obj); } } - goto GOOD; -BAD: + goto __PYX_GOOD; +__PYX_BAD: if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); ret = -1; -GOOD: +__PYX_GOOD: #if !CYTHON_USE_PYTYPE_LOOKUP Py_XDECREF(object_reduce); Py_XDECREF(object_reduce_ex); @@ -113484,7 +112852,7 @@ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { goto done; } -/* CythonFunction */ +/* CythonFunctionShared */ #include static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) @@ -113791,10 +113159,9 @@ static PyMethodDef __pyx_CyFunction_methods[] = { #else #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func.m_weakreflist) #endif -static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, - PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { - __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); - if (op == NULL) +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { + if (unlikely(op == NULL)) return NULL; op->flags = flags; __Pyx_CyFunction_weakreflist(op) = NULL; @@ -113815,12 +113182,12 @@ static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int f Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; + op->defaults_size = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_kwdict = NULL; op->defaults_getter = NULL; op->func_annotations = NULL; - PyObject_GC_Track(op); return (PyObject *) op; } static int @@ -114050,6 +113417,9 @@ static PyTypeObject __pyx_CyFunctionType_type = { #if PY_VERSION_HEX >= 0x030800b1 0, #endif +#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, +#endif }; static int __pyx_CyFunction_init(void) { __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); @@ -114065,6 +113435,7 @@ static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t return PyErr_NoMemory(); memset(m->defaults, 0, size); m->defaults_pyobjects = pyobjects; + m->defaults_size = size; return m->defaults; } static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { @@ -114085,20 +113456,23 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py /* FusedFunction */ static PyObject * -__pyx_FusedFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, - PyObject *qualname, PyObject *self, +__pyx_FusedFunction_New(PyMethodDef *ml, int flags, + PyObject *qualname, PyObject *closure, PyObject *module, PyObject *globals, PyObject *code) { - __pyx_FusedFunctionObject *fusedfunc = - (__pyx_FusedFunctionObject *) __Pyx_CyFunction_New(type, ml, flags, qualname, - self, module, globals, code); - if (!fusedfunc) - return NULL; - fusedfunc->__signatures__ = NULL; - fusedfunc->type = NULL; - fusedfunc->self = NULL; - return (PyObject *) fusedfunc; + PyObject *op = __Pyx_CyFunction_Init( + PyObject_GC_New(__pyx_CyFunctionObject, __pyx_FusedFunctionType), + ml, flags, qualname, closure, module, globals, code + ); + if (likely(op)) { + __pyx_FusedFunctionObject *fusedfunc = (__pyx_FusedFunctionObject *) op; + fusedfunc->__signatures__ = NULL; + fusedfunc->type = NULL; + fusedfunc->self = NULL; + PyObject_GC_Track(op); + } + return op; } static void __pyx_FusedFunction_dealloc(__pyx_FusedFunctionObject *self) @@ -114138,7 +113512,7 @@ __pyx_FusedFunction_descr_get(PyObject *self, PyObject *obj, PyObject *type) } if (obj == Py_None) obj = NULL; - meth = (__pyx_FusedFunctionObject *) __pyx_FusedFunction_NewEx( + meth = (__pyx_FusedFunctionObject *) __pyx_FusedFunction_New( ((PyCFunctionObject *) func)->m_ml, ((__pyx_CyFunctionObject *) func)->flags, ((__pyx_CyFunctionObject *) func)->func_qualname, @@ -114148,6 +113522,20 @@ __pyx_FusedFunction_descr_get(PyObject *self, PyObject *obj, PyObject *type) ((__pyx_CyFunctionObject *) func)->func_code); if (!meth) return NULL; + if (func->func.defaults) { + PyObject **pydefaults; + int i; + if (!__Pyx_CyFunction_InitDefaults((PyObject*)meth, + func->func.defaults_size, + func->func.defaults_pyobjects)) { + Py_XDECREF((PyObject*)meth); + return NULL; + } + memcpy(meth->func.defaults, func->func.defaults, func->func.defaults_size); + pydefaults = __Pyx_CyFunction_Defaults(PyObject *, meth); + for (i = 0; i < meth->func.defaults_pyobjects; i++) + Py_XINCREF(pydefaults[i]); + } Py_XINCREF(func->func.func_classobj); meth->func.func_classobj = func->func.func_classobj; Py_XINCREF(func->__signatures__); @@ -114183,27 +113571,29 @@ __pyx_FusedFunction_getitem(__pyx_FusedFunctionObject *self, PyObject *idx) if (PyTuple_Check(idx)) { PyObject *list = PyList_New(0); Py_ssize_t n = PyTuple_GET_SIZE(idx); - PyObject *string = NULL; PyObject *sep = NULL; int i; - if (!list) + if (unlikely(!list)) return NULL; for (i = 0; i < n; i++) { + int ret; + PyObject *string; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS PyObject *item = PyTuple_GET_ITEM(idx, i); #else - PyObject *item = PySequence_ITEM(idx, i); + PyObject *item = PySequence_ITEM(idx, i); if (unlikely(!item)) goto __pyx_err; #endif string = _obj_to_str(item); #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) Py_DECREF(item); #endif - if (!string || PyList_Append(list, string) < 0) - goto __pyx_err; + if (unlikely(!string)) goto __pyx_err; + ret = PyList_Append(list, string); Py_DECREF(string); + if (unlikely(ret < 0)) goto __pyx_err; } sep = PyUnicode_FromString("|"); - if (sep) + if (likely(sep)) signature = PyUnicode_Join(sep, list); __pyx_err: ; @@ -114407,8 +113797,12 @@ static PyTypeObject __pyx_FusedFunctionType_type = { #if PY_VERSION_HEX >= 0x030800b1 0, #endif +#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, +#endif }; static int __pyx_FusedFunction_init(void) { + __pyx_FusedFunctionType_type.tp_base = __pyx_CyFunctionType; __pyx_FusedFunctionType = __Pyx_FetchCommonType(&__pyx_FusedFunctionType_type); if (__pyx_FusedFunctionType == NULL) { return -1; @@ -114418,7 +113812,7 @@ static int __pyx_FusedFunction_init(void) { /* CLineInTraceback */ #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { +static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int c_line) { PyObject *use_cline; PyObject *ptype, *pvalue, *ptraceback; #if CYTHON_COMPILING_IN_CPYTHON @@ -114522,7 +113916,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } @@ -114626,7 +114020,6 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); @@ -114640,7 +114033,6 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return; } if ((0)) {} - else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); view->obj = NULL; Py_DECREF(obj); } @@ -114785,6 +114177,7 @@ static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { + case '?': return "'bool'"; case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; @@ -114827,7 +114220,7 @@ static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { - case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); @@ -114911,7 +114304,7 @@ static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; - case 'B': case 'H': case 'I': case 'L': case 'Q': + case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); @@ -115055,9 +114448,7 @@ static PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->ndim; -; + int i = 0, number, ndim; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, @@ -115065,6 +114456,7 @@ __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ndim = ctx->head->field->type->ndim; while (*ts && *ts != ')') { switch (*ts) { case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; @@ -115190,12 +114582,12 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha return NULL; } CYTHON_FALLTHROUGH; - case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 'p': - if (ctx->enc_type == *ts && got_Z == ctx->is_complex && - ctx->enc_packmode == ctx->new_packmode) { + if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && + (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { ctx->enc_count += ctx->new_count; ctx->new_count = 1; got_Z = 0; @@ -115281,13 +114673,13 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) if (buf->strides) { if (spec & __Pyx_MEMVIEW_CONTIG) { if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (buf->strides[dim] != sizeof(void *)) { + if (unlikely(buf->strides[dim] != sizeof(void *))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly contiguous " "in dimension %d.", dim); goto fail; } - } else if (buf->strides[dim] != buf->itemsize) { + } else if (unlikely(buf->strides[dim] != buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -115298,7 +114690,7 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) Py_ssize_t stride = buf->strides[dim]; if (stride < 0) stride = -stride; - if (stride < buf->itemsize) { + if (unlikely(stride < buf->itemsize)) { PyErr_SetString(PyExc_ValueError, "Buffer and memoryview are not contiguous " "in the same dimension."); @@ -115306,17 +114698,17 @@ __pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) } } } else { - if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not contiguous in " "dimension %d", dim); goto fail; - } else if (spec & (__Pyx_MEMVIEW_PTR)) { + } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { PyErr_Format(PyExc_ValueError, "C-contiguous buffer is not indirect in " "dimension %d", dim); goto fail; - } else if (buf->suboffsets) { + } else if (unlikely(buf->suboffsets)) { PyErr_SetString(PyExc_ValueError, "Buffer exposes suboffsets but no strides"); goto fail; @@ -115330,7 +114722,7 @@ static int __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) { if (spec & __Pyx_MEMVIEW_DIRECT) { - if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { PyErr_Format(PyExc_ValueError, "Buffer not compatible with direct access " "in dimension %d.", dim); @@ -115338,7 +114730,7 @@ __pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec } } if (spec & __Pyx_MEMVIEW_PTR) { - if (!buf->suboffsets || (buf->suboffsets[dim] < 0)) { + if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { PyErr_Format(PyExc_ValueError, "Buffer is not indirectly accessible " "in dimension %d.", dim); @@ -115356,9 +114748,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) if (c_or_f_flag & __Pyx_IS_F_CONTIG) { Py_ssize_t stride = 1; for (i = 0; i < ndim; i++) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) - { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not fortran contiguous."); goto fail; @@ -115368,8 +114758,7 @@ __pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { Py_ssize_t stride = 1; for (i = ndim - 1; i >- 1; i--) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) { + if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { PyErr_SetString(PyExc_ValueError, "Buffer not C contiguous."); goto fail; @@ -115410,7 +114799,7 @@ static int __Pyx_ValidateAndInit_memviewslice( goto fail; } buf = &memview->view; - if (buf->ndim != ndim) { + if (unlikely(buf->ndim != ndim)) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", ndim, buf->ndim); @@ -115418,9 +114807,9 @@ static int __Pyx_ValidateAndInit_memviewslice( } if (new_memview) { __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; } - if ((unsigned) buf->itemsize != dtype->size) { + if (unlikely((unsigned) buf->itemsize != dtype->size)) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", @@ -115433,12 +114822,12 @@ static int __Pyx_ValidateAndInit_memviewslice( } for (i = 0; i < ndim; i++) { spec = axes_specs[i]; - if (!__pyx_check_strides(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) goto fail; - if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) goto fail; } - if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) goto fail; if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, new_memview != NULL) == -1)) { @@ -116567,7 +115956,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_uint64_t(const char case 1: return a; case 2: - z = __Pyx_c_prod_float(a, a); return __Pyx_c_prod_float(a, a); case 3: z = __Pyx_c_prod_float(a, a); @@ -116722,7 +116110,6 @@ static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_uint64_t(const char case 1: return a; case 2: - z = __Pyx_c_prod_double(a, a); return __Pyx_c_prod_double(a, a); case 3: z = __Pyx_c_prod_double(a, a); @@ -116840,7 +116227,7 @@ __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, struct __pyx_memoryview_obj *memview_obj = NULL; __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); for (i = 0; i < ndim; i++) { - if (from_mvs->suboffsets[i] >= 0) { + if (unlikely(from_mvs->suboffsets[i] >= 0)) { PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " "indirect dimensions (axis %d)", i); goto fail; diff --git a/appveyor.yml b/appveyor.yml index a9a7ab66..17026543 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -19,14 +19,15 @@ environment: - PYTHON: "C:\\Python37-x64" PYTHON_VERSION: "3.7" + - PYTHON: "C:\\Python38-x64" + PYTHON_VERSION: "3.8" + install: - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%" - "%CMD_IN_ENV% python -m pip install -U pip setuptools wheel" - - "%CMD_IN_ENV% python -m pip install cython==0.29.10" - - "%CMD_IN_ENV% python -m pip install numpy==1.16.4" - - "%CMD_IN_ENV% python -m pip install -rrequirements_dev.txt" + - "%CMD_IN_ENV% python -m pip install -rrequirements_dev_base.txt" + - "%CMD_IN_ENV% python -m pip install -rrequirements_dev_optional.txt" - "%CMD_IN_ENV% python -m pip install -rrequirements_test.txt" - - "%CMD_IN_ENV% python -m pip install pyfasta==0.5.2" - "%CMD_IN_ENV% python setup.py build_ext --inplace" build: off diff --git a/docs/release.rst b/docs/release.rst index d843e57c..d0fdd9b3 100644 --- a/docs/release.rst +++ b/docs/release.rst @@ -1,6 +1,16 @@ Release notes ============= + +.. _release_1.3.1: + +v1.3.1 +------ + +* Add compatibility with Python 3.8. By :user:`Alistair Miles + `, :issue:`329`. + + .. _release_1.3.0: v1.3.0 diff --git a/requirements_dev_base.txt b/requirements_dev_base.txt new file mode 100644 index 00000000..6fb07896 --- /dev/null +++ b/requirements_dev_base.txt @@ -0,0 +1,4 @@ +# required +cython==0.29.20 +numpy==1.19.0 +dask[array]==2.19.0 diff --git a/requirements_dev.txt b/requirements_dev_optional.txt similarity index 83% rename from requirements_dev.txt rename to requirements_dev_optional.txt index e52fde22..42fd0ceb 100644 --- a/requirements_dev.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,3 @@ -# required -cython==0.29.20 -numpy==1.19.0 -dask[array]==2.19.0 # optional scipy==1.5.0 matplotlib==3.2.2 @@ -16,3 +12,4 @@ hmmlearn==0.2.3 # install problems on windows, skip for now # https://github.com/jmschrei/pomegranate/issues/333#issuecomment-449151227 #pomegranate==0.10.0 +pyfasta==0.5.2 diff --git a/tox.ini b/tox.ini index adaf204f..4c13f610 100644 --- a/tox.ini +++ b/tox.ini @@ -4,7 +4,7 @@ # and then run "tox" from this directory. [tox] -envlist = py35, py36, py37, docs +envlist = py36, py37, py38, docs # trick to enable pre-installation of numpy and cython indexserver = preinstall = https://pypi.python.org/simple @@ -15,17 +15,16 @@ setenv = PYTHONHASHSEED = 42 commands = python setup.py build_ext --inplace - py35,py36: pytest -v --cov=allel allel - py37: pytest -v --cov=allel --doctest-modules allel + py36,py37: pytest -v --cov=allel allel + py38: pytest -v --cov=allel --doctest-modules allel coverage report -m - py37: flake8 allel --max-line-length=100 + py38: flake8 allel --max-line-length=100 pip freeze deps = :preinstall: setuptools - :preinstall: cython==0.29.10 - :preinstall: numpy==1.16.4 + :preinstall: -rrequirements_dev_base.txt -rrequirements_test.txt - -rrequirements_dev.txt + -rrequirements_dev_optional.txt [testenv:docs] install_command = pip install -U --no-cache-dir {opts} {packages}