Fixed: bamtools coverage not flushing at end (issue #64)

diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp
index c0ecd8f455034c0b3918b5f83be33b637e1f6326..6a4493de9992a5366f12e4997cd12dffeb2adcde 100644 (file)
--- a/src/toolkit/bamtools_coverage.cpp
+++ b/src/toolkit/bamtools_coverage.cpp
@@ -2,7 +2,7 @@
 // bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 24 July 2013
 // ---------------------------------------------------------------------------
 // Prints coverage data for a single BAM file 
 // ***************************************************************************
@@ -137,6 +137,7 @@ bool CoverageTool::CoverageToolPrivate::Run(void) {
     BamAlignment al;    
     while ( reader.GetNextAlignment(al) ) 
         pileup.AddAlignment(al);
+    pileup.Flush();
     
     // clean up 
     reader.Close();