X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ftoolkit%2Fbamtools_sort.cpp;h=f4950588d95f72431906be62f96f4c682812962d;hb=2e1822c9ed231b25fd474117a01a1492d4209fa4;hp=fb181a8b7566abd8b47b0574c78a0b332a84319c;hpb=72f5b82ad353b4cc9d6f8153f1ad19cc387b9597;p=bamtools.git

diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp
index fb181a8..f495058 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: 14 June 2011 (DB)
+// Last modified: 3 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Sorts an input BAM file
 // ***************************************************************************
@@ -40,6 +40,12 @@ const unsigned int SORT_DEFAULT_MAX_BUFFER_MEMORY = 1024;    // Mb
 
 struct SortLessThanPosition {
     bool operator() (const BamAlignment& lhs, const BamAlignment& rhs) {
+
+        // force unmapped alignments to end
+        if ( lhs.RefID == -1 ) return false;
+        if ( rhs.RefID == -1 ) return true;
+
+        // sort first on RefID, then by Position
         if ( lhs.RefID != rhs.RefID )
             return lhs.RefID < rhs.RefID;
         else
@@ -160,7 +166,7 @@ bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
     vector<BamAlignment> buffer;
     buffer.reserve( (size_t)(m_settings->MaxBufferCount*1.1) );
     bool bufferFull = false;
-    
+
     // if sorting by name, we need to generate full char data
     // so can't use GetNextAlignmentCore()
     if ( m_settings->IsSortingByName ) {
@@ -267,12 +273,6 @@ bool SortTool::SortToolPrivate::MergeSortedRuns(void) {
         return false;
     }
 
-    // set sort order for merge
-    if ( m_settings->IsSortingByName )
-        multiReader.SetSortOrder(BamMultiReader::SortedByReadName);
-    else
-        multiReader.SetSortOrder(BamMultiReader::SortedByPosition);
-    
     // open writer for our completely sorted output BAM file
     BamWriter mergedWriter;
     if ( !mergedWriter.Open(m_settings->OutputBamFilename, m_headerText, m_references) ) {
@@ -287,7 +287,7 @@ bool SortTool::SortToolPrivate::MergeSortedRuns(void) {
     while ( multiReader.GetNextAlignmentCore(al) )
         mergedWriter.SaveAlignment(al);
   
-    // close readers
+    // close files
     multiReader.Close();
     mergedWriter.Close();
     
@@ -299,6 +299,7 @@ bool SortTool::SortToolPrivate::MergeSortedRuns(void) {
         remove(tempFilename.c_str());
     }
   
+    // return success
     return true;
 }