Fixed regression: improper @SQ line ordering in SamHeader output

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

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index d56be583e01311cd7a8432936f675c94555ac496..3e2ddd5b022ac309a3f5e0dce80f8d36754485be 100644 (file)
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -10,40 +10,82 @@ 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)
 
-# create main BamTools API library
-add_library( BamTools SHARED
-             BamAlignment.cpp
-             BamIndex.cpp
-             BamMultiReader.cpp
-             BamReader.cpp
-             BamWriter.cpp
-             BGZF.cpp
-             internal/BamReader_p.cpp
-             internal/BamStandardIndex_p.cpp
-             internal/BamToolsIndex_p.cpp
-             internal/BamWriter_p.cpp
-           )
-
-# link BamTools library with zlib automatically
-target_link_libraries( BamTools z )
+# list of all BamTools API source (.cpp) files
+set( BamToolsAPISources
+        BamAlignment.cpp
+        BamMultiReader.cpp
+        BamReader.cpp
+        BamWriter.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
+)
+
+# create main BamTools API shared library
+add_library( BamTools SHARED ${BamToolsAPISources} )
+set_target_properties( BamTools PROPERTIES SOVERSION "2.0.3" )
+set_target_properties( BamTools PROPERTIES OUTPUT_NAME "bamtools" )
 
-# set BamTools library properties
-set_target_properties( BamTools PROPERTIES
-                       SOVERSION   0.9.0
-                       OUTPUT_NAME bamtools
-                     )
+# create main BamTools API static library
+add_library( BamTools-static STATIC ${BamToolsAPISources} )
+set_target_properties( BamTools-static PROPERTIES OUTPUT_NAME "bamtools" )
+set_target_properties( BamTools-static PROPERTIES PREFIX "lib" )
 
-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools")
+# link libraries with zlib automatically
+target_link_libraries( BamTools z )
+target_link_libraries( BamTools-static z )
+
+# set library install destinations
+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 BamAlignment.h   ${ApiIncludeDir})
-ExportHeader(APIHeaders BamAux.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 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 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})