From 1b6d41db1d2f66680620c1af78581f3b1d2a0d6e Mon Sep 17 00:00:00 2001
From: Derek Barnett <derekwbarnett@gmail.com>
Date: Wed, 24 Jul 2013 14:37:50 -0400
Subject: [PATCH] Fixed: bamtools coverage not flushing at end (issue #64)

---
 src/toolkit/bamtools_coverage.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp
index c0ecd8f..6a4493d 100644
--- 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();
-- 
2.39.2