From: derek <derekwbarnett@gmail.com>
Date: Tue, 27 Mar 2012 16:03:54 +0000 (-0400)
Subject: Fixed: sorting order lost during merge step of sort tool, if input BAM
X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=commitdiff_plain;h=76bb08a359f3974eee3e96327b965ccf7958ed1a

Fixed: sorting order lost during merge step of sort tool, if input BAM
lacked SAM header
 * Due to lack of SO tag in temp files. This tag is set just fine on
input BAMs containing SAM headers. However, when an input file lacked
one, especially the (required) VN number, the entire @HD line was
dropped.
 * Forcing the current SAM version number, if none exists, on sort
output.
---

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8deded9..96d3467 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,7 +32,7 @@ ensure_out_of_source_build( "
 # set BamTools version information
 set( BamTools_VERSION_MAJOR 2 )
 set( BamTools_VERSION_MINOR 1 )
-set( BamTools_VERSION_BUILD 0 )
+set( BamTools_VERSION_BUILD 1 )
 
 # set our library and executable destination dirs
 set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h
index 405668c..4bb7ee9 100644
--- a/src/api/SamConstants.h
+++ b/src/api/SamConstants.h
@@ -2,7 +2,7 @@
 // SamConstants.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 27 March 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides constants for SAM header
 // ***************************************************************************
@@ -24,6 +24,8 @@ const char SAM_STAR   = '*';
 const char SAM_TAB    = '\t';
 const std::string SAM_DIGITS = "0123456789";
 
+const std::string SAM_CURRENT_VERSION = "1.4";
+
 // HD entries
 const std::string SAM_HD_BEGIN_TOKEN    = "@HD";
 const std::string SAM_HD_VERSION_TAG    = "VN";
diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
index 58f3697..a88cf79 100644
--- 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  2.1.0
+                       VERSION  2.1.1
                        OUTPUT_NAME "bamtools"
                      )
 # make version info available in application
diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp
index 03143e1..e268bee 100644
--- a/src/toolkit/bamtools_sort.cpp
+++ b/src/toolkit/bamtools_sort.cpp
@@ -2,7 +2,7 @@
 // bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 11 October 2011 (DB)
+// Last modified: 27 March 2012 (DB)
 // ---------------------------------------------------------------------------
 // Sorts an input BAM file
 // ***************************************************************************
@@ -133,6 +133,8 @@ bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
     
     // get basic data that will be shared by all temp/output files 
     SamHeader header = reader.GetHeader();
+    if ( !header.HasVersion() )
+        header.Version = Constants::SAM_CURRENT_VERSION;
     header.SortOrder = ( m_settings->IsSortingByName
                        ? Constants::SAM_HD_SORTORDER_QUERYNAME
                        : Constants::SAM_HD_SORTORDER_COORDINATE );