X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=blobdiff_plain;f=src%2Fapi%2FCMakeLists.txt;h=a9dd0924a2925e7c661f71e6267b02489961b943;hp=7f9b34432d4041c2ee7ed90c847348260b5c0460;hb=71065ecaf5951e21ca202138e7013fce5d634b88;hpb=f63f2faca4e20277fcca2a6b4f8bc627f3dae2bd

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index 7f9b344..a9dd092 100644
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -10,53 +10,58 @@ 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
+# fetch all internal source files
+add_subdirectory( internal )
+
+# make list of all API source 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
+        ${InternalSources}
 )
 
 # 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 OUTPUT_NAME "bamtools" )
+set_target_properties( BamTools PROPERTIES
+                       SOVERSION "2.2.3"
+                       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" )
+set_target_properties( BamTools-static PROPERTIES 
+                       OUTPUT_NAME "bamtools" 
+                       PREFIX "lib" )
+
+# link libraries automatically with zlib (and Winsock2, if applicable)
+if( WIN32 )
+    set( APILibs z ws2_32 )
+else()
+    set( APILibs z )
+endif()
 
-# link libraries with zlib automatically
-target_link_libraries( BamTools z )
-target_link_libraries( BamTools-static z )
+target_link_libraries( BamTools ${APILibs} )
+target_link_libraries( BamTools-static ${APILibs} )
 
 # 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})
@@ -64,10 +69,15 @@ 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} )