tskit update to C_1.1.2

treerec/_README

@@ -8,6 +8,7 @@ The code in `tskit/kastore` is from [kastore/c](https://github.com/tskit-dev/kas
 
 **Changelog:**
 
+- *7 November 2023*: updated to tskit C_1.1.2 (=0.5.5) and kastore 0.3.2)
 - *2 June 2022*: updated to tskit C_1.0.0 and kastore C_2.1.1
 - *5 September 2020*: updated to tskit C_0.99.5
 - *27 August 2020*: updated to tskit C_0.99.5

treerec/tskit/core.c

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2022 Tskit Developers
+ * Copyright (c) 2019-2023 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -222,6 +222,10 @@ tsk_strerror_internal(int err)
         case TSK_ERR_SEEK_OUT_OF_BOUNDS:
             ret = "Tree seek position out of bounds. (TSK_ERR_SEEK_OUT_OF_BOUNDS)";
             break;
+        case TSK_ERR_KEEP_ROWS_MAP_TO_DELETED:
+            ret = "One of the kept rows in the table refers to a deleted row. "
+                  "(TSK_ERR_KEEP_ROWS_MAP_TO_DELETED)";
+            break;
 
         /* Edge errors */
         case TSK_ERR_NULL_PARENT:
@@ -265,7 +269,8 @@ tsk_strerror_internal(int err)
             break;
         case TSK_ERR_BAD_EDGES_CONTRADICTORY_CHILDREN:
             ret = "Bad edges: contradictory children for a given parent over "
-                  "an interval. (TSK_ERR_BAD_EDGES_CONTRADICTORY_CHILDREN)";
+                  "an interval, or indexes need to be rebuilt. "
+                  "(TSK_ERR_BAD_EDGES_CONTRADICTORY_CHILDREN)";
             break;
         case TSK_ERR_CANT_PROCESS_EDGES_WITH_METADATA:
             ret = "Can't squash, flush, simplify or link ancestors with edges that have "
@@ -336,7 +341,7 @@ tsk_strerror_internal(int err)
             ret = "Duplicate sample value. (TSK_ERR_DUPLICATE_SAMPLE)";
             break;
         case TSK_ERR_BAD_SAMPLES:
-            ret = "Bad sample configuration provided. (TSK_ERR_BAD_SAMPLES)";
+            ret = "The nodes provided are not samples. (TSK_ERR_BAD_SAMPLES)";
             break;
 
         /* Table errors */
@@ -350,8 +355,13 @@ tsk_strerror_internal(int err)
         case TSK_ERR_TABLES_NOT_INDEXED:
             ret = "Table collection must be indexed. (TSK_ERR_TABLES_NOT_INDEXED)";
             break;
+        case TSK_ERR_TABLES_BAD_INDEXES:
+            ret = "Table collection indexes inconsistent: do they need to be rebuilt? "
+                  "(TSK_ERR_TABLES_BAD_INDEXES)";
+            break;
         case TSK_ERR_TABLE_OVERFLOW:
-            ret = "Table too large; cannot allocate more than 2**31 rows. "
+            ret = "Table too large; cannot allocate more than 2**31 rows. This error "
+                  "is often caused by a lack of simplification when simulating. "
                   "(TSK_ERR_TABLE_OVERFLOW)";
             break;
         case TSK_ERR_COLUMN_OVERFLOW:
@@ -408,6 +418,14 @@ tsk_strerror_internal(int err)
             ret = "A tree sequence can't take ownership of tables with "
                   "TSK_NO_EDGE_METADATA. (TSK_ERR_CANT_TAKE_OWNERSHIP_NO_EDGE_METADATA)";
             break;
+        case TSK_ERR_UNDEFINED_NONBINARY:
+            ret = "Operation undefined for nonbinary trees. "
+                  "(TSK_ERR_UNDEFINED_NONBINARY)";
+            break;
+        case TSK_ERR_UNDEFINED_MULTIROOT:
+            ret = "Operation undefined for trees that are not singly-rooted. "
+                  "(TSK_ERR_UNDEFINED_MULTIROOT)";
+            break;
 
         /* Stats errors */
         case TSK_ERR_BAD_NUM_WINDOWS:
@@ -500,7 +518,8 @@ tsk_strerror_internal(int err)
             break;
         case TSK_ERR_NO_SAMPLE_LISTS:
             ret = "The sample_lists option must be enabled on the tree to perform this "
-                  "operation. (TSK_ERR_NO_SAMPLE_LISTS)";
+                  "operation. Pass the option to the constructor or method that created "
+                  "the tree. (TSK_ERR_NO_SAMPLE_LISTS)";
             break;
 
         /* Haplotype matching errors */
@@ -571,6 +590,18 @@ tsk_strerror_internal(int err)
             ret = "Individuals cannot be their own ancestor. "
                   "(TSK_ERR_INDIVIDUAL_PARENT_CYCLE)";
             break;
+
+        case TSK_ERR_INDIVIDUAL_POPULATION_MISMATCH:
+            ret = "Individual populations cannot be returned "
+                  "if an individual has nodes from more than one population. "
+                  "(TSK_ERR_INDIVIDUAL_POPULATION_MISMATCH)";
+            break;
+
+        case TSK_ERR_INDIVIDUAL_TIME_MISMATCH:
+            ret = "Individual times cannot be returned "
+                  "if an individual has nodes from more than one time. "
+                  "(TSK_ERR_INDIVIDUAL_TIME_MISMATCH)";
+            break;
     }
     return ret;
 }

treerec/tskit/core.h

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2022 Tskit Developers
+ * Copyright (c) 2019-2023 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -123,6 +123,15 @@ specify options to API functions.
 typedef uint32_t tsk_flags_t;
 #define TSK_FLAGS_STORAGE_TYPE KAS_UINT32
 
+/**
+@brief Boolean type.
+
+@rst
+Fixed-size (1 byte) boolean values.
+@endrst
+*/
+typedef uint8_t tsk_bool_t;
+
 // clang-format off
 /**
 @defgroup API_VERSION_GROUP API version macros.
@@ -138,12 +147,12 @@ sizes and types of externally visible structs.
 The library minor version. Incremented when non-breaking backward-compatible changes
 to the API or ABI are introduced, i.e., the addition of a new function.
 */
-#define TSK_VERSION_MINOR   0
+#define TSK_VERSION_MINOR   1
 /**
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define TSK_VERSION_PATCH   0
+#define TSK_VERSION_PATCH   2
 /** @} */
 
 /*
@@ -172,12 +181,12 @@ Used in node flags to indicate that a node is a sample node.
 */
 #define TSK_NODE_IS_SAMPLE 1u
 
-/** 
+/**
 Null value used for cases such as absent id references.
 */
 #define TSK_NULL ((tsk_id_t) -1)
 
-/** 
+/**
 Value used for missing data in genotype arrays.
 */
 #define TSK_MISSING_DATA    (-1)
@@ -206,7 +215,7 @@ whose representation differs from the NAN generated by computations such as divi
 
 /* Place the common options at the top of the space; this way we can start
 options for individual functions at the bottom without worrying about
-clashing with the common options 
+clashing with the common options
 */
 
 /** Turn on debugging output. Not supported by all functions. */
@@ -224,7 +233,7 @@ behaviour.
 */
 #define TSK_NO_CHECK_INTEGRITY (1u << 29)
 
-/** 
+/**
 Instead of taking a copy of input objects, the function should take ownership
 of them and manage their lifecycle. The caller specifying this flag should no
 longer modify or free the object or objects passed. See individual functions
@@ -356,6 +365,12 @@ A time value was non-finite (NaN counts as finite)
 A genomic position was non-finite
 */
 #define TSK_ERR_GENOME_COORDS_NONFINITE                             -211
+/**
+One of the rows in the retained table refers to a row that has been
+deleted.
+*/
+#define TSK_ERR_KEEP_ROWS_MAP_TO_DELETED                            -212
+
 /** @} */
 
 /**
@@ -543,6 +558,10 @@ The table collection contains more than 2**31 trees.
 Metadata was attempted to be set on a table where it is disabled.
 */
 #define TSK_ERR_METADATA_DISABLED                                   -706
+/**
+There was an error with the table's indexes.
+*/
+#define TSK_ERR_TABLES_BAD_INDEXES                                  -707
 /** @} */
 
 /**
@@ -595,13 +614,22 @@ A tree sequence cannot take ownership of a table collection where
 TSK_NO_EDGE_METADATA.
 */
 #define TSK_ERR_CANT_TAKE_OWNERSHIP_NO_EDGE_METADATA                -809
+/**
+Operation is undefined for nonbinary trees
+*/
+#define TSK_ERR_UNDEFINED_NONBINARY                                 -810
+/**
+Operation is undefined for trees with multiple roots.
+*/
+#define TSK_ERR_UNDEFINED_MULTIROOT                                 -811
+
 /** @} */
 
 /**
 @defgroup STATS_ERROR_GROUP Stats errors.
 @{
 */
-/** 
+/**
 Zero windows were specified, at least one window must be specified.
 */
 #define TSK_ERR_BAD_NUM_WINDOWS                                     -900
@@ -653,17 +681,17 @@ were ``uncalibrated``.
 @defgroup MAPPING_ERROR_GROUP Mutation mapping errors.
 @{
 */
-/** 
+/**
 Only missing genotypes were specified, at least one non-missing is
 required.
 */
 #define TSK_ERR_GENOTYPES_ALL_MISSING                              -1000
-/** 
+/**
 A genotype value was greater than the maximum allowed (64) or less
 than TSK_MISSING_DATA (-1).
 */
 #define TSK_ERR_BAD_GENOTYPE                                       -1001
-/** 
+/**
 A ancestral genotype value was greater than the maximum allowed (64) or less
 than 0.
 */
@@ -760,7 +788,7 @@ specified table collection.
 /**
 The shared portions of the specified tree sequences are not equal.
 Note that this may be the case if the table collections were not
-fully sorted before union was called. 
+fully sorted before union was called.
 */
 #define TSK_ERR_UNION_DIFF_HISTORIES                               -1401
 /** @} */
@@ -812,6 +840,16 @@ An individual was its own parent.
 An individual was its own ancestor in a cycle of references.
 */
 #define TSK_ERR_INDIVIDUAL_PARENT_CYCLE                            -1702
+/**
+An individual had nodes from more than one population
+(and only one was requested).
+*/
+#define TSK_ERR_INDIVIDUAL_POPULATION_MISMATCH                     -1703
+/**
+An individual had nodes from more than one time
+(and only one was requested).
+*/
+#define TSK_ERR_INDIVIDUAL_TIME_MISMATCH                           -1704
 /** @} */
 // clang-format on
 

treerec/tskit/genotypes.c

@@ -463,7 +463,6 @@ tsk_variant_decode(
     tsk_id_t allele_index;
     tsk_size_t j, num_missing;
     int no_longer_missing;
-
     tsk_mutation_t mutation;
     bool impute_missing = !!(self->options & TSK_ISOLATED_NOT_MISSING);
     bool by_traversal = self->alt_samples != NULL;
@@ -485,7 +484,7 @@ tsk_variant_decode(
         goto out;
     }
 
-    /* When we have a no specified samples we need sample lists to be active
+    /* When we have no specified samples we need sample lists to be active
      * on the tree, as indicated by the presence of left_sample */
     if (!by_traversal && self->tree.left_sample == NULL) {
         ret = TSK_ERR_NO_SAMPLE_LISTS;
@@ -582,11 +581,11 @@ tsk_variant_restricted_copy(const tsk_variant_t *self, tsk_variant_t *other)
     tsk_size_t total_len, offset, j;
 
     /* Copy everything */
-    tsk_memcpy(other, self, sizeof(tsk_variant_t));
+    tsk_memcpy(other, self, sizeof(*other));
     /* Tree sequence left as NULL and zero'd tree is a way of indicating this variant is
      * fixed and cannot be further decoded. */
     other->tree_sequence = NULL;
-    tsk_memset(&other->tree, sizeof(tsk_tree_t), 0);
+    tsk_memset(&other->tree, sizeof(other->tree), 0);
     other->traversal_stack = NULL;
     other->samples = NULL;
     other->sample_index_map = NULL;
@@ -598,27 +597,32 @@ tsk_variant_restricted_copy(const tsk_variant_t *self, tsk_variant_t *other)
     for (j = 0; j < self->num_alleles; j++) {
         total_len += self->allele_lengths[j];
     }
-    other->genotypes = tsk_malloc(other->num_samples * sizeof(int32_t));
-    other->user_alleles_mem = tsk_malloc(total_len * sizeof(char *));
+    other->samples = tsk_malloc(other->num_samples * sizeof(*other->samples));
+    other->genotypes = tsk_malloc(other->num_samples * sizeof(*other->genotypes));
+    other->user_alleles_mem = tsk_malloc(total_len * sizeof(*other->user_alleles_mem));
     other->allele_lengths
         = tsk_malloc(other->num_alleles * sizeof(*other->allele_lengths));
     other->alleles = tsk_malloc(other->num_alleles * sizeof(*other->alleles));
-    if (other->genotypes == NULL || other->user_alleles_mem == NULL
-        || other->allele_lengths == NULL || other->alleles == NULL) {
+    if (other->samples == NULL || other->genotypes == NULL
+        || other->user_alleles_mem == NULL || other->allele_lengths == NULL
+        || other->alleles == NULL) {
         ret = TSK_ERR_NO_MEMORY;
         goto out;
     }
-
-    tsk_memcpy(other->genotypes, self->genotypes, other->num_samples * sizeof(int32_t));
+    tsk_memcpy(
+        other->samples, self->samples, other->num_samples * sizeof(*other->samples));
+    tsk_memcpy(other->genotypes, self->genotypes,
+        other->num_samples * sizeof(*other->genotypes));
     tsk_memcpy(other->allele_lengths, self->allele_lengths,
         other->num_alleles * sizeof(*other->allele_lengths));
     offset = 0;
     for (j = 0; j < other->num_alleles; j++) {
         tsk_memcpy(other->user_alleles_mem + offset, self->alleles[j],
-            other->allele_lengths[j] * sizeof(char *));
+            other->allele_lengths[j] * sizeof(*other->user_alleles_mem));
         other->alleles[j] = other->user_alleles_mem + offset;
         offset += other->allele_lengths[j];
     }
+
 out:
     return ret;
 }

treerec/tskit/haplotype_matching.c

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2022 Tskit Developers
+ * Copyright (c) 2019-2023 Tskit Developers
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -250,7 +250,7 @@ tsk_ls_hmm_reset(tsk_ls_hmm_t *self)
 
     /* This is safe because we've already zero'd out the memory. */
     tsk_diff_iter_free(&self->diffs);
-    ret = tsk_diff_iter_init(&self->diffs, self->tree_sequence, false);
+    ret = tsk_diff_iter_init_from_ts(&self->diffs, self->tree_sequence, false);
     if (ret != 0) {
         goto out;
     }