Cleaned up intra-API includes & moved version numbers to 2.0.0

[bamtools.git] / src / api / CMakeLists.txt

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index 9e41c720408cb81a520f44d9e10c1ec27eaa6f74..c85b71b740f532c6814442f2a6625ad20aacad14 100644 (file)
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -10,25 +10,38 @@ include_directories( ${BamTools_SOURCE_DIR}/src )
 
 # 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/BamDeviceFactory_p.cpp
+        internal/BamException_p.cpp
+        internal/BamFile_p.cpp
+        internal/BamFtp_p.cpp
+        internal/BamHeader_p.cpp
+        internal/BamHttp_p.cpp
+        internal/BamIndexFactory_p.cpp
         internal/BamMultiReader_p.cpp
+        internal/BamPipe_p.cpp
+        internal/BamRandomAccessController_p.cpp
         internal/BamReader_p.cpp
         internal/BamStandardIndex_p.cpp
         internal/BamToolsIndex_p.cpp
         internal/BamWriter_p.cpp
+        internal/BgzfStream_p.cpp
+        internal/ILocalIODevice_p.cpp
+        internal/IRemoteIODevice_p.cpp
         internal/SamFormatParser_p.cpp
         internal/SamFormatPrinter_p.cpp
         internal/SamHeaderValidator_p.cpp
@@ -36,7 +49,7 @@ set( BamToolsAPISources
 
 # create main BamTools API shared library
 add_library( BamTools SHARED ${BamToolsAPISources} )
-set_target_properties( BamTools PROPERTIES SOVERSION "0.9.1" )
+set_target_properties( BamTools PROPERTIES SOVERSION "2.0.0" )
 set_target_properties( BamTools PROPERTIES OUTPUT_NAME "bamtools" )
 
 # create main BamTools API static library
@@ -49,23 +62,30 @@ target_link_libraries( BamTools z )
 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})