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)