Cleanup missed by earlier "includes cleanup" commit

[bamtools.git] / src / toolkit / bamtools_convert.cpp

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index 802580201c958b3ebf77a602a4003a2eb0fd7fcf..907c4bafc7357cde60940f3737f120ff6a4aebf8 100644 (file)
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 8 October 2011
 // ---------------------------------------------------------------------------
 // Converts between BAM and a number of other formats
 // ***************************************************************************
@@ -278,7 +277,7 @@ void ConvertTool::ConvertToolPrivate::PrintBed(const BamAlignment& a) {
 
     m_out << m_references.at(a.RefID).RefName << "\t"
           << a.Position << "\t"
-          << a.GetEndPosition() + 1 << "\t"
+          << a.GetEndPosition() << "\t"
           << a.Name << "\t"
           << a.MapQuality << "\t"
           << (a.IsReverseStrand() ? "-" : "+") << endl;
@@ -295,7 +294,7 @@ void ConvertTool::ConvertToolPrivate::PrintFasta(const BamAlignment& a) {
     // N.B. - QueryBases are reverse-complemented if aligned to reverse strand
   
     // print header
-    m_out << "> " << a.Name << endl;
+    m_out << ">" << a.Name << endl;
     
     // handle reverse strand alignment - bases 
     string sequence = a.QueryBases;