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Copy pathCMakeLists_sse4.1.txt
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CMakeLists_sse4.1.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 -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread -lrt") # the -mavx* is for GNU compiler and xCORE* are for intel compiler
set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -pthread -lrt")
#for google unit test
add_subdirectory(./googletest/googletest)
include_directories(googletest/googletest/include googletest/googletest)
add_executable(anchorwave
googletest
googletest/googletest
main.cpp
src/controlLayer.cpp
src/controlLayer.h
src/InputParser.cpp
src/InputParser.h
src/version.h
src/impl/deNovoGenomeVariantCallingMultipleThreads.cpp
src/impl/deNovoGenomeVariantCalling.h
src/impl/geneSyntenic.cpp
src/impl/geneSyntenic.h
src/impl/GetReverseComplementary.cpp
src/impl/GetReverseComplementary.h
src/impl/getSequencesFromGff.cpp
src/impl/getSequencesFromGff.h
src/impl/getSubsequence.cpp
src/impl/getSubsequence.h
src/impl/readFastaFile.cpp
src/impl/readFastaFile.h
src/impl/readGffFile.cpp
src/impl/readGffFile.h
src/impl/TranscriptUpdateInformation.cpp
src/impl/TranscriptUpdateInformation.h
src/model/AlignmentMatch.cpp
src/model/AlignmentMatch.h
src/model/GenomeBasicFeature.cpp
src/model/GenomeBasicFeature.h
src/model/Score.cpp
src/model/Score.h
src/model/STRAND.cpp
src/model/STRAND.h
src/model/Transcript.cpp
src/model/Transcript.h
src/myImportandFunction/alignSlidingWindow.cpp
src/myImportandFunction/alignSlidingWindow.h
src/service/TransferGffWithNucmerResult.cpp
src/service/TransferGffWithNucmerResult.h
src/util/myutil.cpp
src/util/myutil.h
WFA2-lib/alignment/affine2p_penalties.c
WFA2-lib/alignment/affine_penalties.c
WFA2-lib/alignment/cigar.c
WFA2-lib/alignment/score_matrix.c
WFA2-lib/system/mm_allocator.c
WFA2-lib/system/mm_stack.c
WFA2-lib/system/profiler_counter.c
WFA2-lib/system/profiler_timer.c
WFA2-lib/utils/bitmap.c
WFA2-lib/utils/commons.c
WFA2-lib/utils/dna_text.c
WFA2-lib/utils/heatmap.c
WFA2-lib/utils/sequence_buffer.c
WFA2-lib/utils/string_padded.c
WFA2-lib/utils/vector.c
WFA2-lib/wavefront/wavefront_align.c
WFA2-lib/wavefront/wavefront_aligner.c
WFA2-lib/wavefront/wavefront_attributes.c
WFA2-lib/wavefront/wavefront_backtrace_buffer.c
WFA2-lib/wavefront/wavefront_backtrace.c
WFA2-lib/wavefront/wavefront_backtrace_offload.c
WFA2-lib/wavefront/wavefront_bialign.c
WFA2-lib/wavefront/wavefront.c
WFA2-lib/wavefront/wavefront_components.c
WFA2-lib/wavefront/wavefront_compute_affine2p.c
WFA2-lib/wavefront/wavefront_compute_affine.c
WFA2-lib/wavefront/wavefront_compute.c
WFA2-lib/wavefront/wavefront_compute_edit.c
WFA2-lib/wavefront/wavefront_compute_linear.c
WFA2-lib/wavefront/wavefront_debug.c
WFA2-lib/wavefront/wavefront_display.c
WFA2-lib/wavefront/wavefront_extend.c
WFA2-lib/wavefront/wavefront_heuristic.c
WFA2-lib/wavefront/wavefront_pcigar.c
WFA2-lib/wavefront/wavefront_penalties.c
WFA2-lib/wavefront/wavefront_plot.c
WFA2-lib/wavefront/wavefront_slab.c
WFA2-lib/wavefront/wavefront_unialign.c
WFA2-lib/wavefront/wavefront_unialign.h
WFA2-lib/wavefront/wavefront_bialigner.c
WFA2-lib/wavefront/wavefront_bialigner.h
WFA2-lib/alignment/affine2p_penalties.h
WFA2-lib/alignment/affine_penalties.h
WFA2-lib/alignment/cigar.h
WFA2-lib/alignment/linear_penalties.h
WFA2-lib/alignment/score_matrix.h
WFA2-lib/scripts/fasta2seq.sh
WFA2-lib/scripts/seq2fasta.sh
WFA2-lib/scripts/wfa.alg.cmp.score.sh
WFA2-lib/system/mm_allocator.h
WFA2-lib/system/mm_stack.h
WFA2-lib/system/profiler_counter.h
WFA2-lib/system/profiler_timer.h
WFA2-lib/utils/bitmap.h
WFA2-lib/utils/commons.h
WFA2-lib/utils/dna_text.h
WFA2-lib/utils/heatmap.h
WFA2-lib/utils/sequence_buffer.h
WFA2-lib/utils/string_padded.h
WFA2-lib/utils/vector.h
WFA2-lib/wavefront/wavefront_aligner.h
WFA2-lib/wavefront/wavefront_align.h
WFA2-lib/wavefront/wavefront_attributes.h
WFA2-lib/wavefront/wavefront_backtrace_buffer.h
WFA2-lib/wavefront/wavefront_backtrace.h
WFA2-lib/wavefront/wavefront_backtrace_offload.h
WFA2-lib/wavefront/wavefront_bialign.h
WFA2-lib/wavefront/wavefront_components.h
WFA2-lib/wavefront/wavefront_compute_affine2p.h
WFA2-lib/wavefront/wavefront_compute_affine.h
WFA2-lib/wavefront/wavefront_compute_edit.h
WFA2-lib/wavefront/wavefront_compute.h
WFA2-lib/wavefront/wavefront_compute_linear.h
WFA2-lib/wavefront/wavefront_debug.h
WFA2-lib/wavefront/wavefront_display.h
WFA2-lib/wavefront/wavefront_extend.h
WFA2-lib/wavefront/wavefront.h
WFA2-lib/wavefront/wavefront_heuristic.h
WFA2-lib/wavefront/wavefront_offset.h
WFA2-lib/wavefront/wavefront_pcigar.h
WFA2-lib/wavefront/wavefront_penalties.h
WFA2-lib/wavefront/wavefront_plot.h
WFA2-lib/wavefront/wavefront_slab.h
WFA2-lib/bindings/cpp/WFAligner.cpp
WFA2-lib/bindings/cpp/WFAligner.hpp
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
)
target_link_libraries(anchorwave gtest gtest_main ZLIB::ZLIB)
install(TARGETS anchorwave DESTINATION bin)