# add compiler definitions
add_definitions( -DBAMTOOLS_API_LIBRARY ) # (for proper exporting of library symbols)
+add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
# list of all BamTools API source (.cpp) files
set( BamToolsAPISources
BamAlignment.cpp
- BamIndex.cpp
BamMultiReader.cpp
BamReader.cpp
BamWriter.cpp
- BGZF.cpp
SamHeader.cpp
+ SamProgram.cpp
+ SamProgramChain.cpp
SamReadGroup.cpp
SamReadGroupDictionary.cpp
SamSequence.cpp
SamSequenceDictionary.cpp
- internal/BamHeader_p.cpp
- internal/BamMultiReader_p.cpp
- internal/BamReader_p.cpp
- internal/BamStandardIndex_p.cpp
- internal/BamToolsIndex_p.cpp
- internal/BamWriter_p.cpp
- internal/SamFormatParser_p.cpp
- internal/SamFormatPrinter_p.cpp
- internal/SamHeaderValidator_p.cpp
+ internal/bam/BamHeader_p.cpp
+ internal/bam/BamMultiReader_p.cpp
+ internal/bam/BamRandomAccessController_p.cpp
+ internal/bam/BamReader_p.cpp
+ internal/bam/BamWriter_p.cpp
+ internal/index/BamIndexFactory_p.cpp
+ internal/index/BamStandardIndex_p.cpp
+ internal/index/BamToolsIndex_p.cpp
+ internal/io/BamDeviceFactory_p.cpp
+ internal/io/BamFile_p.cpp
+ internal/io/BamFtp_p.cpp
+ internal/io/BamHttp_p.cpp
+ internal/io/BamPipe_p.cpp
+ internal/io/BgzfStream_p.cpp
+ internal/io/ILocalIODevice_p.cpp
+ internal/io/IRemoteIODevice_p.cpp
+ internal/sam/SamFormatParser_p.cpp
+ internal/sam/SamFormatPrinter_p.cpp
+ internal/sam/SamHeaderValidator_p.cpp
+ internal/utils/BamException_p.cpp
)
# create main BamTools API shared library
add_library( BamTools SHARED ${BamToolsAPISources} )
-set_target_properties( BamTools PROPERTIES SOVERSION "0.9.3" )
+set_target_properties( BamTools PROPERTIES SOVERSION "2.0.5" )
set_target_properties( BamTools PROPERTIES OUTPUT_NAME "bamtools" )
# create main BamTools API static library
target_link_libraries( BamTools-static z )
# set library install destinations
-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools")
+install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
# export API headers
include(../ExportHeader.cmake)
set(ApiIncludeDir "api")
ExportHeader(APIHeaders api_global.h ${ApiIncludeDir})
+ExportHeader(APIHeaders BamAlgorithms.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamAlignment.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamAux.h ${ApiIncludeDir})
+ExportHeader(APIHeaders BamConstants.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamIndex.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamMultiReader.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamReader.h ${ApiIncludeDir})
ExportHeader(APIHeaders BamWriter.h ${ApiIncludeDir})
-ExportHeader(APIHeaders BGZF.h ${ApiIncludeDir})
+ExportHeader(APIHeaders IBamIODevice.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamConstants.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamHeader.h ${ApiIncludeDir})
+ExportHeader(APIHeaders SamProgram.h ${ApiIncludeDir})
+ExportHeader(APIHeaders SamProgramChain.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamReadGroup.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamReadGroupDictionary.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamSequence.h ${ApiIncludeDir})
ExportHeader(APIHeaders SamSequenceDictionary.h ${ApiIncludeDir})
+
+set(AlgorithmsIncludeDir "api/algorithms")
+ExportHeader(AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir})