# if haven't defined our custom 'build target'
# not exactly a build target, but lets this command get
# checked any time build step happens
- if (NOT TARGET ${MODULE})
+ if( NOT TARGET ${MODULE} )
add_custom_target( ${MODULE} ALL COMMENT "Exporting ${MODULE}" )
- endif (NOT TARGET ${MODULE} )
+ endif( NOT TARGET ${MODULE} )
# get the filename (without path)
get_filename_component( FILENAME "${FILE}" NAME )
"${CMAKE_CURRENT_SOURCE_DIR}/${FILE}"
"${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" )
-
-
# make sure files are properly 'installed'
- # set(INSTALL_DEST "bamtools/${DEST}")
- # install( FILES "${FILE}" DESTINATION "${INSTALL_DEST}")
install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
endfunction( ExportHeader )
PREFIX "lib" )
# link libraries with zlib automatically
-if ( _WIN32 )
+if( _WIN32 )
set( APILibs z ws2_32 )
-else ( _WIN32 )
+else( _WIN32 )
set( APILibs z )
-endif ( _WIN32 )
+endif( _WIN32 )
target_link_libraries( BamTools ${APILibs} )
target_link_libraries( BamTools-static ${APILibs} )
# src/api/internal
# ==========================
-set ( InternalDir "internal" )
+set( InternalDir "internal" )
-add_subdirectory ( bam )
-add_subdirectory ( index )
-add_subdirectory ( io )
-add_subdirectory ( sam )
-add_subdirectory ( utils )
+add_subdirectory( bam )
+add_subdirectory( index )
+add_subdirectory( io )
+add_subdirectory( sam )
+add_subdirectory( utils )
-set ( InternalSources
- ${InternalBamSources}
- ${InternalIndexSources}
- ${InternalIOSources}
- ${InternalSamSources}
- ${InternalUtilsSources}
+set( InternalSources
+ ${InternalBamSources}
+ ${InternalIndexSources}
+ ${InternalIOSources}
+ ${InternalSamSources}
+ ${InternalUtilsSources}
- PARENT_SCOPE # <-- leave this last
- )
+ PARENT_SCOPE # <-- leave this last
+ )
// BamReader_p.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-<<<<<<< HEAD:src/api/internal/BamReader_p.cpp
-// Last modified: 14 November 2011 (DB)
-=======
-// Last modified: 25 October 2011 (DB)
->>>>>>> remoteio:src/api/internal/bam/BamReader_p.cpp
+// Last modified: 28 November 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
# src/api/internal/bam
# ==========================
-set ( InternalBamDir "${InternalDir}/bam" )
+set( InternalBamDir "${InternalDir}/bam" )
-set ( InternalBamSources
- ${InternalBamDir}/BamHeader_p.cpp
- ${InternalBamDir}/BamMultiReader_p.cpp
- ${InternalBamDir}/BamRandomAccessController_p.cpp
- ${InternalBamDir}/BamReader_p.cpp
- ${InternalBamDir}/BamWriter_p.cpp
+set( InternalBamSources
+ ${InternalBamDir}/BamHeader_p.cpp
+ ${InternalBamDir}/BamMultiReader_p.cpp
+ ${InternalBamDir}/BamRandomAccessController_p.cpp
+ ${InternalBamDir}/BamReader_p.cpp
+ ${InternalBamDir}/BamWriter_p.cpp
- PARENT_SCOPE # <-- leave this last
-)
+ PARENT_SCOPE # <-- leave this last
+ )
#define BAMINDEX_FACTORYTEST_H
#include "api/BamIndex.h"
-#include "api/internal/BamIndexFactory_p.h"
-#include "api/internal/BamStandardIndex_p.h"
-#include "api/internal/BamToolsIndex_p.h"
+#include "api/internal/index/BamIndexFactory_p.h"
+#include "api/internal/index/BamStandardIndex_p.h"
+#include "api/internal/index/BamToolsIndex_p.h"
#include <gtest/gtest.h>
#include <iostream>
#define BAMSTANDARDINDEX_TEST_H
#include <gtest/gtest.h>
-#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/index/BamStandardIndex_p.h"
TEST(BamStandardIndexTest, Open) {