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2. Adjust CMakeLists.txt parameters
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,70 +1,71 @@ | ||
| cmake_minimum_required(VERSION 2.8.4) | ||
| project(VerifyBamID) | ||
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| set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin") | ||
| set(CMAKE_CXX_STANDARD 11) | ||
| set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -Wno-format-security") | ||
| set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -Wno-unused-variable -Wno-unused-result ") | ||
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| add_definitions(-D__STDC_LIMIT_MACROS) | ||
| add_definitions(-D__ZLIB_AVAILABLE__) | ||
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| find_path(HTS_INCLUDE_DIRS htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT HTS_INCLUDE_DIRS ) | ||
| message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found") | ||
| endif() | ||
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| find_library(HTS_LIBRARIES hts HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT HTS_LIBRARIES) | ||
| message(FATAL_ERROR "libhts HTS_LIBRARIES not found") | ||
| endif() | ||
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| find_package(OpenMP) | ||
| if (OPENMP_FOUND) | ||
| set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") | ||
| set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") | ||
| endif() | ||
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| find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT ZLIB) | ||
| message(FATAL_ERROR "libz library not found") | ||
| endif() | ||
| find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT CURLLIB) | ||
| message(FATAL_ERROR "libcurl library not found") | ||
| endif() | ||
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| find_package (BZip2) | ||
| if (NOT BZIP2_FOUND) | ||
| message(FATAL_ERROR "libbz2 library not found") | ||
| else() | ||
| include_directories(${BZIP2_INCLUDE_DIRS}) | ||
| set(BZIP2 ${BZIP2_LIBRARIES}) | ||
| endif() | ||
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| find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT LZMA) | ||
| message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning") | ||
| set(LZMA "") | ||
| else() | ||
| set(LZMA ${LZMA_LIBRARIES}) | ||
| endif() | ||
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| add_subdirectory(statgen) | ||
| set(LIBSTATGEN_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/statgen") | ||
| add_subdirectory(samtools) | ||
| add_subdirectory(libVcf) | ||
| set(SOURCE_FILES main.cpp SVDcalculator.cpp ContaminationEstimator.cpp MathGenMin.cpp MathGold.cpp Random.cpp SimplePileupViewer.cpp params.cpp ) | ||
| include_directories(statgen ${HTS_INCLUDE_DIRS} samtools libVcf Eigen) | ||
| add_executable(VerifyBamID ${SOURCE_FILES}) | ||
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| target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB} ${BZIP2} ${LZMA} ${CURLLIB}) | ||
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| enable_testing() | ||
| add_test( NAME myTest1 | ||
| WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | ||
| COMMAND VerifyBamID --DisableSanityCheck --UDPath resource/test/hapmap_3.3.b37.dat.UD --BamFile resource/test/test.bam --BedPath resource/test/hapmap_3.3.b37.dat.bed --MeanPath resource/test/hapmap_3.3.b37.dat.mu --Reference resource/test/chr20.fa.gz ) | ||
| #add_test( NAME myTest2 | ||
| # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | ||
| # COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey) | ||
| cmake_minimum_required(VERSION 2.8.4) | ||
| project(VerifyBamID) | ||
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| set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin") | ||
| set(CMAKE_CXX_STANDARD 11) | ||
| set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -fPIC -Wno-format-security") | ||
| set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -fPIC -Wno-unused-variable -Wno-unused-result ") | ||
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| add_definitions(-D__STDC_LIMIT_MACROS) | ||
| add_definitions(-D__ZLIB_AVAILABLE__) | ||
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| find_package(OpenMP) | ||
| if (OPENMP_FOUND) | ||
| set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") | ||
| set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") | ||
| endif () | ||
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||
| find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if (NOT CURLLIB) | ||
| message(FATAL_ERROR "libcurl library not found") | ||
| endif () | ||
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| find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ /usr/local/Cellar/zlib/1.2.11/lib/) | ||
| if (NOT ZLIB) | ||
| message(FATAL_ERROR "libz library not found") | ||
| endif () | ||
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| find_path(HTS_INCLUDE_DIRS htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if (NOT HTS_INCLUDE_DIRS) | ||
| message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found") | ||
| endif () | ||
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| find_library(HTS_LIBRARIES hts HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if (NOT HTS_LIBRARIES) | ||
| message(FATAL_ERROR "libhts HTS_LIBRARIES not found") | ||
| endif () | ||
|
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||
| find_package(BZip2) | ||
| if (NOT BZIP2_FOUND) | ||
| message(FATAL_ERROR "libbz2 library not found") | ||
| else () | ||
| include_directories(${BZIP2_INCLUDE_DIRS}) | ||
| set(BZIP2 ${BZIP2_LIBRARIES}) | ||
| endif () | ||
|
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| find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/) | ||
| if(NOT LZMA) | ||
| message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning") | ||
| set(LZMA "") | ||
| else() | ||
| set(LZMA ${LZMA_LIBRARIES}) | ||
| endif() | ||
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| add_subdirectory(statgen) | ||
| set(LIBSTATGEN_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/statgen") | ||
| add_subdirectory(samtools) | ||
| add_subdirectory(libVcf) | ||
| set(SOURCE_FILES main.cpp SVDcalculator.cpp ContaminationEstimator.cpp MathGenMin.cpp MathGold.cpp Random.cpp SimplePileupViewer.cpp params.cpp ) | ||
| include_directories(statgen ${HTS_INCLUDE_DIRS} samtools libVcf Eigen) | ||
| add_executable(VerifyBamID ${SOURCE_FILES}) | ||
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| target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB} ${BZIP2} ${LZMA} ${CURLLIB}) | ||
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| enable_testing() | ||
| add_test( NAME myTest1 | ||
| WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | ||
| COMMAND VerifyBamID --DisableSanityCheck --UDPath resource/test/hapmap_3.3.b37.dat.UD --BamFile resource/test/test.bam --BedPath resource/test/hapmap_3.3.b37.dat.bed --MeanPath resource/test/hapmap_3.3.b37.dat.mu --Reference resource/test/chr20.fa.gz ) | ||
| #add_test( NAME myTest2 | ||
| # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | ||
| # COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey) |
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