Add cmake project file.

CMakeLists.txt

@@ -0,0 +1,94 @@
+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)