version RC3.0

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.0)
+project(anchorwave)
+
+#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()
+
+find_package(ZLIB)
+
+set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -I ./ -std=gnu++14 -pthread")
+set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -I ./ -pthread")
+#for google unit test
+add_subdirectory(./googletest/googletest)
+include_directories(googletest/googletest/include googletest/googletest)
+
+
+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/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/TEGffToAlignment.cpp
+#        src/tests/impl/CompareSdiAlignmentWithMafFile
+        src/service/TransferGffWithNucmerResult.cpp
+        src/service/TransferGffWithNucmerResult.h
+        src/service/Reformat.cpp
+        src/service/Reformat.h
+        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/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
+
+        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
+
+        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
+
+        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_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
+
+        src/service/Reformat.cpp src/service/Reformat.h src/service/evaluation.cpp src/service/evaluation.h src/version.h)
+
+target_link_libraries(anchorwave gtest gtest_main ZLIB::ZLIB)
+
+#
+#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})

FAQ.md

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+## My machine with built-in gcc <6. Even if I set LD_LIBRARY_PATH and PATH to use new gcc, the source code still tried to use old gcc in /usr/bin and failed compilation.
+The key is setting LD_LIBRARY_PATH and PATH before typing `cmake ./`. The easiest way maybe:  
+1) Delete the current source code using commands `rm -rf anchorwave`.  
+2) Set `LD_LIBRARY_PATH`, `PATH`, `CC`, and `GCC` to the new gcc.  
+3) Re-clone the AnchorWave repository and compile it.  
+## Should I perform genome repeat masking before feed into AnchorWave
+Genome masking is not expected to improve the performance of AnchorWave.  
+AnchorWave do not utilize any soft masking information. Hard masking would increase the
+computational cost of AnchorWave.

LICENSE

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+MIT License
+
+Copyright (c) 2017 baoxingsong
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.