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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| /figs/ | ||
| /Debug/ | ||
| /Makefile | ||
| /anchorwave | ||
| /cmake_install.cmake | ||
| /CMakeCache.txt | ||
| /cmake-build-debug/ | ||
| /CMakeFiles/ | ||
| /googletest/googletest/CMakeFiles/ | ||
| /googletest/googletest/cmake_install.cmake | ||
| /googletest/googletest/libgtest.a | ||
| /googletest/googletest/libgtest_main.a | ||
| /googletest/googletest/libgtest_maind.a | ||
| /googletest/googletest/libgtestd.a | ||
| /googletest/googletest/Makefile | ||
| *.log | ||
| *.a | ||
| *.o | ||
| /googletest/googletest/CMakeFiles/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,258 @@ | ||
| cmake_minimum_required(VERSION 3.0) | ||
| project(anchorwave) | ||
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| #include(CheckCXXCompilerFlag) | ||
| set(CMAKE_CXX_STANDARD 14) | ||
| # | ||
| #if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") | ||
| # set(MACOSX TRUE) | ||
| ##else() | ||
| ## set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") | ||
| #endif() | ||
|
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| find_package(ZLIB) | ||
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| # | ||
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| set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -mavx2 -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread") # the -mavx* is for GNU compiler and xCORE* are for intel compiler | ||
| set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -mavx2 -msse4.1 -msse4.2 -I ./ -pthread") | ||
| #for google unit test | ||
| add_subdirectory(./googletest/googletest) | ||
| include_directories(googletest/googletest/include googletest/googletest) | ||
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| add_executable(anchorwave | ||
| googletest | ||
| googletest/googletest | ||
| # ksw2_extz2_sse.c | ||
| # ksw2.h | ||
| # src/myImportandFunction/alignNeedlemanForTranscript_simd.cpp | ||
| src/model/GenomeBasicFeature.cpp | ||
| src/model/GenomeBasicFeature.h | ||
| src/controlLayer.cpp | ||
| src/controlLayer.h | ||
| src/InputParser.cpp | ||
| src/InputParser.h | ||
| src/model/model.h | ||
| src/util/myutil.cpp | ||
| src/util/myutil.h | ||
| src/util/nucleotideCodeSubstitutionMatrix.cpp | ||
| src/util/nucleotideCodeSubstitutionMatrix.h | ||
| src/util/parameters.cpp | ||
| src/util/parameters.h | ||
| main.cpp | ||
| src/model/variant.cpp | ||
| src/model/variant.h | ||
| src/model/Transcript.cpp | ||
| src/model/Transcript.h | ||
| src/model/Gene.cpp | ||
| src/model/Gene.h | ||
| src/model/Matrix.cpp | ||
| src/model/Matrix.h | ||
| src/model/FirstLastList.cpp | ||
| src/model/FirstLastList.h | ||
| src/model/STRAND.h | ||
| src/model/STRAND.cpp | ||
| src/model/Seed.h | ||
| src/model/Seed.cpp | ||
| src/model/PairedSimilarFragment.cpp | ||
| src/model/PairedSimilarFragment.h | ||
| # src/impl/sequenceAlignment.cpp | ||
| # src/impl/sequenceAlignment.h | ||
| src/impl/impl.h | ||
| src/impl/GetReverseComplementary.cpp | ||
| src/impl/GetReverseComplementary.h | ||
| src/impl/readFastaFile.cpp | ||
| src/impl/readFastaFile.h | ||
| src/util/util.h | ||
| src/impl/getSubsequence.cpp | ||
| src/impl/getSubsequence.h | ||
| src/impl/readGffFile.cpp | ||
| src/impl/readGffFile.h | ||
| src/impl/getSequencesFromGff.cpp | ||
| src/impl/getSequencesFromGff.h | ||
| src/service/service.h | ||
| src/myImportandFunction/myImportantFunction.h | ||
| src/impl/TranscriptUpdateInformation.cpp | ||
| src/impl/TranscriptUpdateInformation.h | ||
| src/tests/impl/test_WFA.cpp | ||
| src/tests/impl/readMafForMsa.cpp | ||
| src/tests/impl/TEGffToAlignment.cpp | ||
| src/tests/impl/readGffFile.cpp | ||
| src/tests/impl/readFastaFile_test.cpp | ||
| # src/tests/impl/CompareSdiAlignmentWithMafFile | ||
| src/service/TransferGffWithNucmerResult.cpp | ||
| src/service/TransferGffWithNucmerResult.h | ||
| src/service/Reformat.cpp | ||
| src/service/Reformat.h | ||
| src/service/callVariantFromSamFile.h | ||
| src/service/callVariantFromSamFile.cpp | ||
| src/myImportandFunction/alignSlidingWindow.cpp | ||
| src/myImportandFunction/alignSlidingWindow.h | ||
| src/impl/CheckAndUpdateTranscriptsEnds.cpp | ||
| src/impl/CheckAndUpdateTranscriptsEnds.h | ||
| src/impl/deNovoGenomeVariantCallingMultipleThreads.cpp | ||
| src/impl/deNovoGenomeVariantCalling.h | ||
| src/impl/WriteFasta.cpp | ||
| src/impl/WriteFasta.h | ||
| src/model/AlignmentMatch.cpp | ||
| src/model/AlignmentMatch.h | ||
| src/model/Score.cpp | ||
| src/model/Score.h | ||
| src/impl/geneSyntenic.cpp | ||
| src/impl/geneSyntenic.h | ||
| src/impl/SequenceCharToUInt8.cpp | ||
| src/impl/SequenceCharToUInt8.h | ||
| WFA/alignment/cigar.c | ||
| WFA/alignment/cigar.h | ||
| WFA/alignment/score_matrix.c | ||
| WFA/alignment/score_matrix.h | ||
|
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||
| WFA/system/profiler_counter.c | ||
| WFA/system/profiler_counter.h | ||
| WFA/system/profiler_timer.c | ||
| WFA/system/profiler_timer.h | ||
| WFA/system/mm_allocator.c | ||
| WFA/system/mm_allocator.h | ||
| WFA/system/mm_stack.c | ||
| WFA/system/mm_stack.h | ||
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||
| WFA/benchmark/benchmark_edit.h | ||
| WFA/benchmark/benchmark_gap_affine.c | ||
| WFA/benchmark/benchmark_gap_affine.h | ||
| WFA/benchmark/benchmark_gap_lineal.c | ||
| WFA/benchmark/benchmark_gap_lineal.h | ||
| WFA/benchmark/benchmark_utils.c | ||
| WFA/benchmark/benchmark_utils.h | ||
| WFA/benchmark/benchmark_check.c | ||
| WFA/benchmark/benchmark_check.h | ||
| WFA/benchmark/benchmark_gap_affine2p.c | ||
| WFA/benchmark/benchmark_gap_affine2p.h | ||
| WFA/utils/commons.c | ||
| WFA/utils/commons.h | ||
| WFA/utils/dna_text.c | ||
| WFA/utils/dna_text.h | ||
| WFA/utils/string_padded.c | ||
| WFA/utils/string_padded.h | ||
| WFA/utils/vector.c | ||
| WFA/utils/vector.h | ||
| WFA/gap_affine/affine_penalties.c | ||
| WFA/gap_affine/affine_penalties.h | ||
| WFA/gap_affine/affine_matrix.c | ||
| WFA/gap_affine/affine_matrix.h | ||
| WFA/gap_affine/affine_wavefront_align.c | ||
| WFA/gap_affine/affine_wavefront_align.h | ||
| WFA/gap_affine/affine_wavefront_backtrace.c | ||
| WFA/gap_affine/affine_wavefront_backtrace.h | ||
| WFA/gap_affine/affine_wavefront.c | ||
| WFA/gap_affine/affine_wavefront_display.c | ||
| WFA/gap_affine/affine_wavefront_display.h | ||
| WFA/gap_affine/affine_wavefront_extend.c | ||
| WFA/gap_affine/affine_wavefront_extend.h | ||
| WFA/gap_affine/affine_wavefront.h | ||
| WFA/gap_affine/affine_wavefront_penalties.c | ||
| WFA/gap_affine/affine_wavefront_penalties.h | ||
| WFA/gap_affine/affine_wavefront_reduction.c | ||
| WFA/gap_affine/affine_wavefront_reduction.h | ||
| WFA/gap_affine/affine_wavefront_utils.c | ||
| WFA/gap_affine/affine_wavefront_utils.h | ||
| WFA/gap_affine/swg.c | ||
| WFA/gap_affine/swg.h | ||
| WFA/gap_affine/wavefront_stats.c | ||
| WFA/gap_affine/wavefront_stats.h | ||
| WFA/gap_affine2p/affine2p_dp.c | ||
| WFA/gap_affine2p/affine2p_dp.h | ||
| WFA/gap_affine2p/affine2p_matrix.c | ||
| WFA/gap_affine2p/affine2p_matrix.h | ||
| WFA/gap_affine2p/affine2p_penalties.c | ||
| WFA/gap_affine2p/affine2p_penalties.h | ||
| WFA/gap_affine2p/affine2p_wavefront.c | ||
| WFA/gap_affine2p/affine2p_wavefront.h | ||
| WFA/gap_affine2p/affine2p_wavefront_align.c | ||
| WFA/gap_affine2p/affine2p_wavefront_align.h | ||
| WFA/gap_affine2p/affine2p_wavefront_backtrace.c | ||
| WFA/gap_affine2p/affine2p_wavefront_backtrace.h | ||
| WFA/gap_affine2p/affine2p_wavefront_display.c | ||
| WFA/gap_affine2p/affine2p_wavefront_display.h | ||
| WFA/gap_affine2p/affine2p_wavefront_extend.c | ||
| WFA/gap_affine2p/affine2p_wavefront_extend.h | ||
| WFA/gap_lineal/lineal_penalties.h | ||
| WFA/gap_lineal/nw.c | ||
| WFA/gap_lineal/nw.h | ||
| WFA/edit/edit_dp.c | ||
| WFA/edit/edit_dp.h | ||
| WFA/benchmark/benchmark_edit.c | ||
| WFA/benchmark/benchmark_edit.h | ||
| WFA/benchmark/benchmark_gap_affine.c | ||
| WFA/benchmark/benchmark_gap_affine.h | ||
| WFA/benchmark/benchmark_gap_lineal.c | ||
| WFA/benchmark/benchmark_gap_lineal.h | ||
| WFA/benchmark/benchmark_utils.c | ||
| WFA/benchmark/benchmark_utils.h | ||
|
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| minimap2/align.c | ||
| minimap2/bseq.c | ||
| minimap2/chain.c | ||
| minimap2/esterr.c | ||
| minimap2/format.c | ||
| minimap2/hit.c | ||
| minimap2/index.c | ||
| minimap2/kalloc.c | ||
| minimap2/ksw2_dispatch.c | ||
| minimap2/ksw2_extd2_sse.c | ||
| minimap2/ksw2_extd2_avx.c | ||
| minimap2/ksw2_exts2_sse.c | ||
| minimap2/ksw2_extz2_sse.c | ||
| minimap2/ksw2_ll_sse.c | ||
| minimap2/kthread.c | ||
| minimap2/map.c | ||
| minimap2/misc.c | ||
| minimap2/options.c | ||
| minimap2/pe.c | ||
| minimap2/sdust.c | ||
| minimap2/sketch.c | ||
| minimap2/splitidx.c | ||
| minimap2/sse2neon/emmintrin.h | ||
| minimap2/bseq.h | ||
| minimap2/kalloc.h | ||
| minimap2/kdq.h | ||
| minimap2/ketopt.h | ||
| minimap2/khash.h | ||
| minimap2/kseq.h | ||
| minimap2/ksort.h | ||
| minimap2/ksw2.h | ||
| minimap2/kthread.h | ||
| minimap2/kvec.h | ||
| minimap2/minimap.h | ||
| minimap2/mmpriv.h | ||
| minimap2/sdust.h | ||
| # | ||
| # ksw2/kalloc.h | ||
| # ksw2/kseq.h | ||
| # ksw2/ksw2.h | ||
| #// ksw2/cli.c | ||
| # ksw2/kalloc.c | ||
| # ksw2/ksw2_extd2_sse.c | ||
| # ksw2/ksw2_extd.c | ||
| # ksw2/ksw2_extf2_sse.c | ||
| # ksw2/ksw2_exts2_sse.c | ||
| # ksw2/ksw2_extz2_sse.c | ||
| # ksw2/ksw2_extz.c | ||
| # ksw2/ksw2_gg2.c | ||
| # ksw2/ksw2_gg2_sse.c | ||
| # ksw2/ksw2_gg.c | ||
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| src/service/Reformat.cpp src/service/Reformat.h src/service/evaluation.cpp src/service/evaluation.h src/version.h src/service/callVariantFromSamFile.h src/model/BlocksForMsa.cpp src/model/BlocksForMsa.h src/impl/readMafForMsa.cpp src/impl/readMafForMsa.h src/model/AlignmentBlock.cpp src/model/AlignmentBlock.h src/model/PhylogeneticTreeNode.cpp src/model/PhylogeneticTreeNode.h src/model/PhylogeneticTree.cpp src/model/PhylogeneticTree.h src/tests/model/PhylogeneticTree.cpp src/service/TreeManip.cpp src/service/TreeManip.h src/impl/reconstructAncestorUsingThree.cpp src/impl/reconstructAncestorUsingThree.h src/model/Range.cpp src/model/Range.h src/model/TwoVectorsOfRanges.cpp src/model/TwoVectorsOfRanges.h) | ||
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| target_link_libraries(anchorwave gtest gtest_main ZLIB::ZLIB) | ||
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| # | ||
| #set(MAKE_CMD "/bin/bash") | ||
| #set(MAKE_CMD_ARG1 "${CMAKE_SOURCE_DIR}/compileWFA.sh") | ||
| # | ||
| #MESSAGE("COMMAND: ${MAKE_CMD} ${MAKE_CMD_ARG1}") | ||
| #execute_process(COMMAND ${MAKE_CMD} ${MAKE_CMD_ARG1} | ||
| # RESULT_VARIABLE CMD_ERROR | ||
| # OUTPUT_FILE CMD_OUTPUT) | ||
| #MESSAGE( STATUS "CMD_ERROR:" ${CMD_ERROR}) | ||
| #MESSAGE( STATUS "CMD_OUTPUT:" ${CMD_OUTPUT}) |
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