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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 3.5)
project(bamUtil)
include_directories(${CMAKE_SOURCE_DIR}/../libStatGen/include)
execute_process(COMMAND date OUTPUT_VARIABLE DATE OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND whoami OUTPUT_VARIABLE USER OUTPUT_STRIP_TRAILING_WHITESPACE)
set(VERSION "1.0.14")
set(CMAKE_VERBOSE_MAKEFILE ON)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -DVERSION='\"${VERSION}\"' -DUSER='\"${USER}\"' -DDATE='\"${DATE}\"' -D__ZLIB_AVAILABLE__")
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
set(SOURCE_FILES
src/Bam2FastQ.cpp
src/Bam2FastQ.h
src/BamExecutable.cpp
src/BamExecutable.h
src/ClipOverlap.cpp
src/ClipOverlap.h
src/Convert.cpp
src/Convert.h
src/Covariates.h
src/Dedup.cpp
src/Dedup.h
src/Dedup_LowMem.cpp
src/Dedup_LowMem.h
src/Diff.cpp
src/Diff.h
src/DumpHeader.cpp
src/DumpHeader.h
src/DumpIndex.cpp
src/DumpIndex.h
src/DumpRefInfo.cpp
src/DumpRefInfo.h
src/ExplainFlags.cpp
src/ExplainFlags.h
src/Filter.cpp
src/Filter.h
src/FindCigars.cpp
src/FindCigars.h
src/GapInfo.cpp
src/GapInfo.h
src/HashErrorModel.cpp
src/HashErrorModel.h
src/Logger.cpp
src/Logger.h
src/LogisticRegression.cpp
src/LogisticRegression.h
src/Main.cpp
src/MateMapByCoord.cpp
src/MateMapByCoord.h
src/MathCholesky.cpp
src/MathCholesky.h
src/MergeBam.cpp
src/MergeBam.h
src/OverlapClipLowerBaseQual.cpp
src/OverlapClipLowerBaseQual.h
src/OverlapHandler.cpp
src/OverlapHandler.h
src/PileupElementBaseQCStats.cpp
src/PileupElementBaseQCStats.h
src/PolishBam.cpp
src/PolishBam.h
src/Prediction.cpp
src/Prediction.h
src/ReadIndexedBam.cpp
src/ReadIndexedBam.h
src/ReadReference.cpp
src/ReadReference.h
src/Recab.cpp
src/Recab.h
src/Revert.cpp
src/Revert.h
src/SplitBam.cpp
src/SplitBam.h
src/SplitChromosome.cpp
src/SplitChromosome.h
src/Squeeze.cpp
src/Squeeze.h
src/Stats.cpp
src/Stats.h
src/TrimBam.cpp
src/TrimBam.h
src/Validate.cpp
src/Validate.h
src/WriteRegion.cpp
src/WriteRegion.h)
add_executable(bam ${SOURCE_FILES})
target_link_libraries(bam ${CMAKE_SOURCE_DIR}/../libStatGen/libStatGen.a)
target_link_libraries(bam libz.dylib)