From 29c554c08c72d265bb2110f2fd9019125224b595 Mon Sep 17 00:00:00 2001 From: derek Date: Mon, 28 Nov 2011 19:09:58 -0500 Subject: [PATCH] Post-merge cleanup --- src/ExportHeader.cmake | 8 ++---- src/api/CMakeLists.txt | 6 ++--- src/api/internal/CMakeLists.txt | 28 ++++++++++---------- src/api/internal/bam/BamReader_p.cpp | 6 +---- src/api/internal/bam/CMakeLists.txt | 18 ++++++------- src/test/api/BamIndex/BamIndexFactoryTest.h | 6 ++--- src/test/api/BamIndex/BamStandardIndexTest.h | 2 +- 7 files changed, 33 insertions(+), 41 deletions(-) diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake index d0d8c1e..ec62573 100644 --- a/src/ExportHeader.cmake +++ b/src/ExportHeader.cmake @@ -7,9 +7,9 @@ function( ExportHeader MODULE FILE DEST ) # 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 ) @@ -20,11 +20,7 @@ function( ExportHeader MODULE FILE DEST ) "${CMAKE_CURRENT_SOURCE_DIR}/${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 ) diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 539feca..d559c45 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -44,11 +44,11 @@ set_target_properties( BamTools-static PROPERTIES 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} ) diff --git a/src/api/internal/CMakeLists.txt b/src/api/internal/CMakeLists.txt index 1e7b8dd..a96cd6f 100644 --- a/src/api/internal/CMakeLists.txt +++ b/src/api/internal/CMakeLists.txt @@ -5,21 +5,21 @@ # 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} + ${InternalUtilsSources} - PARENT_SCOPE # <-- leave this last - ) + PARENT_SCOPE # <-- leave this last + ) diff --git a/src/api/internal/bam/BamReader_p.cpp b/src/api/internal/bam/BamReader_p.cpp index 6904da7..75d7279 100644 --- a/src/api/internal/bam/BamReader_p.cpp +++ b/src/api/internal/bam/BamReader_p.cpp @@ -2,11 +2,7 @@ // BamReader_p.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -<<<<<<< HEAD:src/api/internal/BamReader_p.cpp -// Last modified: 14 November 2011 (DB) -======= -// Last modified: 25 October 2011 (DB) ->>>>>>> remoteio:src/api/internal/bam/BamReader_p.cpp +// Last modified: 28 November 2011 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for reading BAM files // *************************************************************************** diff --git a/src/api/internal/bam/CMakeLists.txt b/src/api/internal/bam/CMakeLists.txt index 64d8534..1bd2569 100644 --- a/src/api/internal/bam/CMakeLists.txt +++ b/src/api/internal/bam/CMakeLists.txt @@ -5,15 +5,15 @@ # src/api/internal/bam # ========================== -set ( InternalBamDir "${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 + ) diff --git a/src/test/api/BamIndex/BamIndexFactoryTest.h b/src/test/api/BamIndex/BamIndexFactoryTest.h index ac1538b..f6755df 100644 --- a/src/test/api/BamIndex/BamIndexFactoryTest.h +++ b/src/test/api/BamIndex/BamIndexFactoryTest.h @@ -2,9 +2,9 @@ #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 #include diff --git a/src/test/api/BamIndex/BamStandardIndexTest.h b/src/test/api/BamIndex/BamStandardIndexTest.h index f96af82..ca1aadd 100644 --- a/src/test/api/BamIndex/BamStandardIndexTest.h +++ b/src/test/api/BamIndex/BamStandardIndexTest.h @@ -2,7 +2,7 @@ #define BAMSTANDARDINDEX_TEST_H #include -#include "api/internal/BamStandardIndex_p.h" +#include "api/internal/index/BamStandardIndex_p.h" TEST(BamStandardIndexTest, Open) { -- 2.39.2