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Updated to v2.1.0
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@bbuchfink
bbuchfink committed Jan 25, 2023
1 parent 1938c34 commit 6c91cb4
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Showing 465 changed files with 49,902 additions and 7,068 deletions.
204 changes: 167 additions & 37 deletions CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,13 @@ option(DP_STAT "DP_STAT" OFF)
option(SINGLE_THREADED "SINGLE_THREADED" OFF)
option(EIGEN_BLAS "EIGEN_BLAS" OFF)
option(WITH_ZSTD "WITH_ZSTD" OFF)
option(KEEP_TARGET_ID "KEEP_TARGET_ID" OFF)
option(HIT_KEEP_TARGET_ID "HIT_KEEP_TARGET_ID" OFF)
option(LONG_SEEDS "LONG_SEEDS" OFF)
option(WITH_AVX512 "WITH_AVX512" OFF)
option(WITH_DNA "WITH_DNA" OFF)
option(WITH_MCL "WITH_MCL" OFF)
option(WITH_MIMALLOC "WITH_MIMALLOC" OFF)
set(MAX_SHAPE_LEN 19)
set(BLAST_INCLUDE_DIR "" CACHE STRING "BLAST_INCLUDE_DIR")
set(BLAST_LIBRARY_DIR "" CACHE STRING "BLAST_LIBRARY_DIR")
Expand Down Expand Up @@ -58,16 +65,40 @@ if(EXTRA)
add_definitions(-DEXTRA)
endif()

if(KEEP_TARGET_ID)
add_definitions(-DKEEP_TARGET_ID)
endif()

if(HIT_KEEP_TARGET_ID)
add_definitions(-DHIT_KEEP_TARGET_ID)
endif()

if(LONG_SEEDS)
add_definitions(-DLONG_SEEDS)
endif()

if(WITH_AVX512)
add_definitions(-DWITH_AVX512)
endif()

if(WITH_DNA)
add_definitions(-DWITH_DNA)
endif()

if(WITH_MCL)
add_definitions(-DWITH_MCL)
endif()

add_definitions(-DMAX_SHAPE_LEN=${MAX_SHAPE_LEN})

IF(STATIC_LIBGCC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libgcc")
endif()

if(BUILD_STATIC)
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
set(BUILD_SHARED_LIBRARIES OFF)
set(CMAKE_EXE_LINKER_FLAGS "-static")
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
set(BUILD_SHARED_LIBRARIES OFF)
set(CMAKE_EXE_LINKER_FLAGS "-static")
endif()

check_cxx_compiler_flag("-std=gnu++14" HAS_GNUPP14)
Expand Down Expand Up @@ -113,14 +144,17 @@ if (CMAKE_COMPILER_IS_GNUCC AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
endif()

set(DISPATCH_OBJECTS
"src/dp/swipe/banded_3frame_swipe.cpp"
"src/search/stage2.cpp"
"src/tools/benchmark.cpp"
"src/dp/swipe/swipe_wrapper.cpp"
"src/util/tantan.cpp"
"src/dp/scan_diags.cpp"
"src/dp/ungapped_simd.cpp"
)
"src/dp/swipe/banded_3frame_swipe.cpp"
"src/search/stage2.cpp"
"src/tools/benchmark.cpp"
"src/dp/swipe/swipe_wrapper.cpp"
"src/masking/tantan.cpp"
"src/dp/scan_diags.cpp"
"src/dp/ungapped_simd.cpp"
"src/dp/pfscan/pfscan.cpp"
"src/dp/swipe/anchored_wrapper.cpp"
"src/dp/score_profile.cpp"
)

if(EXTRA)
LIST(APPEND DISPATCH_OBJECTS "src/tools/benchmark_swipe.cpp")
Expand All @@ -130,25 +164,34 @@ add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})
target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC)
target_include_directories(arch_generic PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
if(X86)
add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})
target_include_directories(arch_sse4_1 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
add_library(arch_avx2 OBJECT ${DISPATCH_OBJECTS})
target_include_directories(arch_avx2 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_SSE4_1)
add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})
target_include_directories(arch_sse4_1 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
add_library(arch_avx2 OBJECT ${DISPATCH_OBJECTS})
target_include_directories(arch_avx2 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
if(WITH_AVX512)
add_library(arch_avx512 OBJECT ${DISPATCH_OBJECTS})
target_include_directories(arch_avx512 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
endif()
if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_SSE4_1)
target_compile_options(arch_avx2 PUBLIC -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 /arch:AVX2 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_AVX2)
else()
target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1)
if(WITH_AVX512)
target_compile_options(arch_avx512 PUBLIC -DDISPATCH_ARCH=ARCH_AVX512 -DARCH_ID=3 /arch:AVX512 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_AVX512)
endif()
else()
target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1)
target_compile_options(arch_avx2 PUBLIC -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2)
endif()
if(WITH_AVX512)
target_compile_options(arch_avx512 PUBLIC -DDISPATCH_ARCH=ARCH_AVX512 -DARCH_ID=3 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -mavx512f -mavx512bw -DEigen=Eigen_AVX512)
endif()
endif()
endif(X86)

set(OBJECTS
src/run/main.cpp
src/basic/config.cpp
src/stats/score_matrix.cpp
src/data/queries.cpp
src/data/reference.cpp
src/data/seed_histogram.cpp
src/output/daa/daa_record.cpp
src/util/command_line_parser.cpp
Expand Down Expand Up @@ -204,35 +247,28 @@ set(OBJECTS
src/tools/tools.cpp
src/util/system/getRSS.cpp
src/lib/tantan/LambdaCalculator.cc
src/util/algo/upgma.cpp
src/util/algo/upgma_mc.cpp
src/util/algo/edge_vec.cpp
src/util/string/string.cpp
src/align/extend.cpp
src/test/simulate.cpp
src/test/test.cpp
src/align/ungapped.cpp
src/align/gapped_score.cpp
src/align/gapped_final.cpp
src/align/full_db.cpp
src/align/culling.cpp
src/cluster/medoid.cpp
src/cluster/cluster_registry.cpp
src/cluster/multi_step_cluster.cpp
src/cluster/mcl.cpp
src/cluster/cascaded/cascaded.cpp
src/align/output.cpp
src/tools/roc.cpp
src/test/data.cpp
src/test/test_cases.cpp
src/chaining/smith_waterman.cpp
src/tools/merge_tsv.cpp
src/output/xml_format.cpp
src/align/gapped_filter.cpp
src/util/parallel/filestack.cpp
src/util/parallel/parallelizer.cpp
src/util/parallel/multiprocessing.cpp
src/tools/benchmark_io.cpp
src/align/memory.cpp
src/lib/alp/njn_dynprogprob.cpp
src/lib/alp/njn_dynprogproblim.cpp
src/lib/alp/njn_dynprogprobproto.cpp
Expand Down Expand Up @@ -272,21 +308,104 @@ set(OBJECTS
src/data/dmnd/dmnd.cpp
src/data/sequence_file.cpp
src/tools/find_shapes.cpp
src/data/block.cpp
src/data/block/block.cpp
src/data/block/block_wrapper.cpp
src/run/config.cpp
src/data/sequence_set.cpp
src/align/global_ranking/table.cpp
src/output/daa/daa_write.cpp
src/search/seed_complexity.cpp
src/tools/view.cpp
src/util/string/tsv.cpp
src/util/tsv/tsv.cpp
src/tools/join.cpp
src/basic/value.cpp
src/masking/motifs.cpp
src/align/alt_hsp.cpp
src/data/fasta/fasta_file.cpp
# src/cluster/incremental/run.cpp
src/cluster/output.cpp
# src/cluster/incremental/config.cpp
src/cluster/realign.cpp
src/cluster/reassign.cpp
src/util/tsv/read_tsv.cpp
src/tools/greedy_vertex_cover.cpp
src/cluster/cascaded/recluster.cpp
src/cluster/helpers.cpp
src/util/kmer/filter.cpp
src/align/kmer_filter.cpp
src/search/kmer_ranking.cpp
src/chaining/hamming_ext.cpp
src/dna/smith_watermann.cpp
src/stats/dna_scoring/build_score.cpp
src/lib/blast/blast_message.cpp
src/lib/blast/blast_stat.cpp
src/lib/blast/blastn_score.cpp
src/lib/blast/ncbi_std.cpp
src/util/tsv/table.cpp
src/util/tsv/file.cpp
src/util/tsv/record.cpp
src/cluster/cascaded/helpers.cpp
src/cluster/cascaded/wrapper.cpp
src/output/daa/merge.cpp
src/chaining/backtrace.cpp
src/util/tsv/merge.cpp
src/util/tsv/join.cpp
src/dp/scalar/smith_waterman.cpp
src/cluster/incremental/config.cpp
src/cluster/incremental/run.cpp
src/align/short.cpp
)

if(WITH_DNA)
list(APPEND OBJECTS src/lib/wfa2/alignment/affine2p_penalties.c
src/lib/wfa2/alignment/affine_penalties.c
src/lib/wfa2/alignment/cigar.c
src/lib/wfa2/alignment/score_matrix.c
src/lib/wfa2/bindings/cpp/WFAligner.cpp
src/lib/wfa2/system/mm_allocator.c
src/lib/wfa2/system/mm_stack.c
src/lib/wfa2/system/profiler_counter.c
src/lib/wfa2/system/profiler_timer.c
src/lib/wfa2/utils/bitmap.c
src/lib/wfa2/utils/commons.c
src/lib/wfa2/utils/dna_text.c
src/lib/wfa2/utils/heatmap.c
src/lib/wfa2/utils/sequence_buffer.c
src/lib/wfa2/utils/string_padded.c
src/lib/wfa2/utils/vector.c
src/lib/wfa2/wavefront/wavefront.c
src/lib/wfa2/wavefront/wavefront_align.c
src/lib/wfa2/wavefront/wavefront_aligner.c
src/lib/wfa2/wavefront/wavefront_attributes.c
src/lib/wfa2/wavefront/wavefront_backtrace.c
src/lib/wfa2/wavefront/wavefront_backtrace_buffer.c
src/lib/wfa2/wavefront/wavefront_backtrace_offload.c
src/lib/wfa2/wavefront/wavefront_components.c
src/lib/wfa2/wavefront/wavefront_compute.c
src/lib/wfa2/wavefront/wavefront_compute_affine.c
src/lib/wfa2/wavefront/wavefront_compute_linear.c
src/lib/wfa2/wavefront/wavefront_compute_affine2p.c
src/lib/wfa2/wavefront/wavefront_compute_edit.c
src/lib/wfa2/wavefront/wavefront_debug.c
src/lib/wfa2/wavefront/wavefront_display.c
src/lib/wfa2/wavefront/wavefront_extend.c
src/lib/wfa2/wavefront/wavefront_heuristic.c
src/lib/wfa2/wavefront/wavefront_pcigar.c
src/lib/wfa2/wavefront/wavefront_penalties.c
src/lib/wfa2/wavefront/wavefront_plot.c
src/lib/wfa2/wavefront/wavefront_slab.c
src/dna/smith_watermann.cpp
src/dna/wfa2_test.cpp
src/dna/TEMP_minimap_seeding.cpp
src/lib/wfa2/wavefront/wavefront_unialign.c
src/lib/wfa2/wavefront/wavefront_bialigner.c
src/lib/wfa2/wavefront/wavefront_bialign.c)
endif()

if(WITH_MCL)
list(APPEND OBJECTS src/contrib/mcl/mcl.cpp)
endif()

list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}")

if(BLAST_INCLUDE_DIR)
Expand All @@ -298,14 +417,18 @@ if(WITH_ZSTD OR BLAST_INCLUDE_DIR)
endif()

if(X86)
add_executable(diamond $<TARGET_OBJECTS:arch_generic> $<TARGET_OBJECTS:arch_sse4_1> $<TARGET_OBJECTS:arch_avx2> ${OBJECTS} ${BLAST_OBJ} ${ZSTD_OBJ})
if(WITH_AVX512)
add_executable(diamond $<TARGET_OBJECTS:arch_generic> $<TARGET_OBJECTS:arch_sse4_1> $<TARGET_OBJECTS:arch_avx2> $<TARGET_OBJECTS:arch_avx512> ${OBJECTS} ${BLAST_OBJ} ${ZSTD_OBJ})
else()
add_executable(diamond $<TARGET_OBJECTS:arch_generic> $<TARGET_OBJECTS:arch_sse4_1> $<TARGET_OBJECTS:arch_avx2> ${OBJECTS} ${BLAST_OBJ} ${ZSTD_OBJ})
endif()
else()
add_executable(diamond $<TARGET_OBJECTS:arch_generic> ${OBJECTS} ${BLAST_OBJ} ${ZSTD_OBJ})
endif()

target_include_directories(diamond PRIVATE
"${ZLIB_INCLUDE_DIR}"
"${CMAKE_SOURCE_DIR}/src/lib")
"${ZLIB_INCLUDE_DIR}"
"${CMAKE_SOURCE_DIR}/src/lib")

if(BLAST_INCLUDE_DIR)
function(find_blast_lib var library)
Expand Down Expand Up @@ -338,9 +461,9 @@ if(BLAST_INCLUDE_DIR)
find_blast_lib(XUTIL_LIBRARY xutil)
find_blast_lib(LMDB_LIBRARY lmdb)
target_link_libraries(diamond ${SEQDB_LIBRARY} ${BLASTDB_LIBRARY} ${BLASTDB_FORMAT_LIBRARY} ${GENERAL_LIBRARY}
${XOBJUTIL_LIBRARY} ${XOBJMGR_LIBRARY} ${GENOME_COLLECTION_LIBRARY} ${SEQ_LIBRARY} ${SEQCODE_LIBRARY}
${SEQSET_LIBRARY} ${SEQUTIL_LIBRARY} ${PUB_LIBRARY} ${MEDLINE_LIBRARY} ${BIBLIO_LIBRARY} ${SUBMIT_LIBRARY}
${XSER_LIBRARY} ${XNCBI_LIBRARY} ${XUTIL_LIBRARY} ${LMDB_LIBRARY})
${XOBJUTIL_LIBRARY} ${XOBJMGR_LIBRARY} ${GENOME_COLLECTION_LIBRARY} ${SEQ_LIBRARY} ${SEQCODE_LIBRARY}
${SEQSET_LIBRARY} ${SEQUTIL_LIBRARY} ${PUB_LIBRARY} ${MEDLINE_LIBRARY} ${BIBLIO_LIBRARY} ${SUBMIT_LIBRARY}
${XSER_LIBRARY} ${XNCBI_LIBRARY} ${XUTIL_LIBRARY} ${LMDB_LIBRARY})
add_definitions(-DWITH_BLASTDB)
set_target_properties(diamond PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
Expand All @@ -366,6 +489,13 @@ if(WITH_ZSTD OR BLAST_INCLUDE_DIR)
add_definitions(-DWITH_ZSTD)
endif()

if(WITH_MIMALLOC)
find_package(mimalloc 2.0 REQUIRED)
add_definitions(-DWITH_MIMALLOC)
target_link_libraries(diamond mimalloc)
target_include_directories(diamond PRIVATE ${MIMALLOC_INCLUDE_DIR})
endif()

target_link_libraries(diamond ${ZLIB_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})

install(TARGETS diamond DESTINATION bin)
14 changes: 7 additions & 7 deletions Dockerfile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,20 +2,20 @@ FROM ubuntu:latest as build-diamond

ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=Europe/Moscow
RUN apt-get update && apt-get install -y g++ automake cmake zlib1g-dev subversion libzstd-dev
RUN apt-get update && apt-get install -y g++ automake cmake zlib1g-dev git libzstd-dev

WORKDIR /opt/diamond
ADD . .

RUN svn co https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++
WORKDIR c++
RUN ./cmake-configure --without-debug --with-projects="objtools/blast/seqdb_reader;objtools/blast/blastdb_format"
WORKDIR CMake-GCC930-Release/build
RUN git clone https://github.com/ncbi/ncbi-cxx-toolkit-public.git
WORKDIR ncbi-cxx-toolkit-public
RUN ./cmake-configure --without-debug --with-projects="objtools/blast/seqdb_reader;objtools/blast/blastdb_format" --with-build-root=build
WORKDIR build/build
RUN make -j4
RUN cp /opt/diamond/c++/CMake-GCC930-Release/inc/ncbiconf_unix.h /opt/diamond/c++/include
RUN cp /opt/diamond/ncbi-cxx-toolkit-public/build/inc/ncbiconf_unix.h /opt/diamond/ncbi-cxx-toolkit-public/include

WORKDIR /opt/diamond/build
RUN cmake -DCMAKE_BUILD_TYPE=Release -DBLAST_INCLUDE_DIR=/opt/diamond/c++/include -DBLAST_LIBRARY_DIR=/opt/diamond/c++/CMake-GCC930-Release/lib ..
RUN cmake -DCMAKE_BUILD_TYPE=Release -DBLAST_INCLUDE_DIR=/opt/diamond/ncbi-cxx-toolkit-public/include -DBLAST_LIBRARY_DIR=/opt/diamond/ncbi-cxx-toolkit-public/build/lib ..
RUN make -j4 && make install

FROM ubuntu:latest
Expand Down

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