Minor version bump - 2.3.0

  * stabilized remote file support
  * additional bug fixes & feature requests
  * bamtools-utils & jsoncpp libs now built as static libs by default
(issue #55)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3e81b1a2739605a10175a99bc3f7c639d8c64a26..9b97fa07bb4aa05f646d7f0e8130d479134756fa 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,8 +31,8 @@ ensure_out_of_source_build( "
 
 # set BamTools version information
 set( BamTools_VERSION_MAJOR 2 )
-set( BamTools_VERSION_MINOR 2 )
-set( BamTools_VERSION_BUILD 3 )
+set( BamTools_VERSION_MINOR 3 )
+set( BamTools_VERSION_BUILD 0 )
 
 # set our library and executable destination dirs
 set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )

diff --git a/docs/Doxyfile b/docs/Doxyfile
index ff88c615b9fdb132b0263ef8ca9758989a663810..410ea279baa30cf3860100e0caf84fa65e67db14 100644 (file)
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -31,7 +31,7 @@ PROJECT_NAME           = BamTools
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = 2.2.3
+PROJECT_NUMBER         = 2.3.0
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index a9dd0924a2925e7c661f71e6267b02489961b943..7e3d3ca7812ec8d6417a7cc85f0e2477f1e7bc18 100644 (file)
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -34,7 +34,7 @@ set( BamToolsAPISources
 # create main BamTools API shared library
 add_library( BamTools SHARED ${BamToolsAPISources} )
 set_target_properties( BamTools PROPERTIES
-                       SOVERSION "2.2.3"
+                       SOVERSION "2.3.0"
                        OUTPUT_NAME "bamtools" )
 
 # create main BamTools API static library
@@ -50,11 +50,11 @@ else()
     set( APILibs z )
 endif()
 
-target_link_libraries( BamTools ${APILibs} )
+target_link_libraries( BamTools        ${APILibs} )
 target_link_libraries( BamTools-static ${APILibs} )
 
 # set library install destinations
-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+install( TARGETS BamTools        LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
 install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
 
 # export API headers

diff --git a/src/api/internal/bam/BamMultiReader_p.cpp b/src/api/internal/bam/BamMultiReader_p.cpp
index 08d445d0986aedfa06d4b5939383df0fdebc739f..310d8371241f4650fcb95c66e1977bcc2625ef25 100644 (file)
--- a/src/api/internal/bam/BamMultiReader_p.cpp
+++ b/src/api/internal/bam/BamMultiReader_p.cpp
@@ -2,7 +2,7 @@
 // BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 14 January 2013 (DB)
+// Last modified: 24 July 2013 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -184,7 +184,7 @@ IMultiMerger* BamMultiReaderPrivate::CreateAlignmentCache(void) {
             m_mergeOrder = BamMultiReader::MergeByCoordinate;
 
         // if BAM files are sorted by read name
-        if ( header.SortOrder == Constants::SAM_HD_SORTORDER_QUERYNAME )
+        else if ( header.SortOrder == Constants::SAM_HD_SORTORDER_QUERYNAME )
             m_mergeOrder = BamMultiReader::MergeByName;
 
         // otherwise, sorting is either "unknown" or marked as "unsorted"

diff --git a/src/third_party/jsoncpp/CMakeLists.txt b/src/third_party/jsoncpp/CMakeLists.txt
index 03c091b2197c2aab7bd70c9661cd6019ac376d29..8dc64e43c8cf6aef092b750af337d91ade2dd104 100644 (file)
--- a/src/third_party/jsoncpp/CMakeLists.txt
+++ b/src/third_party/jsoncpp/CMakeLists.txt
@@ -10,7 +10,7 @@ add_definitions( -DBAMTOOLS_JSONCPP_LIBRARY ) # (for proper exporting of library
 add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
 
 # create jsoncpp library
-add_library( jsoncpp SHARED
+add_library( jsoncpp STATIC
              json_reader.cpp
              json_value.cpp
              json_writer.cpp
@@ -18,6 +18,6 @@ add_library( jsoncpp SHARED
 
 # set jsoncpp library properties
 set_target_properties( jsoncpp PROPERTIES
-                       SOVERSION   1.0.0
                        OUTPUT_NAME jsoncpp
+                       PREFIX "lib"
                      )

diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
index 1be9efb7480f655ca1c3cb2e08fae6c4e948f883..33b073544ad92b129e81ac81e3a9a96ed09ac1df 100644 (file)
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
@@ -31,7 +31,7 @@ add_executable( bamtools_cmd
 
 # set BamTools application properties
 set_target_properties( bamtools_cmd PROPERTIES
-                       VERSION  2.2.3
+                       VERSION  2.3.0
                        OUTPUT_NAME "bamtools"
                      )
 # make version info available in application

diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
index 2d91ca39a34e2d63c73528ee0049237f5405d77e..1c33f4b2007b72daa6549bb290e59844afb6b92c 100644 (file)
--- a/src/utils/CMakeLists.txt
+++ b/src/utils/CMakeLists.txt
@@ -13,7 +13,7 @@ add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library s
 add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
 
 # create BamTools utils library
-add_library( BamTools-utils SHARED
+add_library( BamTools-utils STATIC
              bamtools_fasta.cpp
              bamtools_options.cpp
              bamtools_pileup_engine.cpp
@@ -25,6 +25,6 @@ target_link_libraries( BamTools-utils BamTools )
 
 # set BamTools library properties
 set_target_properties( BamTools-utils PROPERTIES
-                       SOVERSION   2.2.0
                        OUTPUT_NAME bamtools-utils
+                       PREFIX "lib"
                      )