Post-merge cleanup

diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake
index d0d8c1ec7501639e72bdc961e610f15b6ea39ac1..ec625734cd4ff9ba3712985df5e6bc67170f40bd 100644 (file)
--- 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 539feca0317a4e801ce14fa34626c0a98849e654..d559c45e084180f796291513ddb9b0847d851468 100644 (file)
--- 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 1e7b8dd54b8b74a213ed8cb6b1acd8c950adfb56..a96cd6fac40eb4dc44b457d4e5bb5946e55b7544 100644 (file)
--- 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 6904da7a6f3f53c917ba6d274521c2aaf6d7208c..75d727928bb6757c49f033ea938e2fa4e81a5f20 100644 (file)
--- 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 64d8534b7eee52847e165c64132197df407ace5d..1bd2569d3ecdb9f207f7eae566a979557ee10cc0 100644 (file)
--- 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 ac1538b75a2db244e5a5a1703344fd1f274ea373..f6755df7f8dd467ed15833ec621571e73c3cff23 100644 (file)
--- 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 <gtest/gtest.h>
 #include <iostream>

diff --git a/src/test/api/BamIndex/BamStandardIndexTest.h b/src/test/api/BamIndex/BamStandardIndexTest.h
index f96af8204b5fa0fa60b6d9f4d64483bafbab3f50..ca1aadd47e3a95543f0fab3f8203e17143f05f73 100644 (file)
--- a/src/test/api/BamIndex/BamStandardIndexTest.h
+++ b/src/test/api/BamIndex/BamStandardIndexTest.h
@@ -2,7 +2,7 @@
 #define BAMSTANDARDINDEX_TEST_H
 
 #include <gtest/gtest.h>
-#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/index/BamStandardIndex_p.h"
 
 TEST(BamStandardIndexTest, Open) {