Version 2.5.4 (Mar-3-2010)

	Fixed an insidious bug that caused malformed BAM output from intersectBed and pairToBed.  The previous BAM files worked fine with samtools as BAM input, but when piped in as SAM, there was an extra tab that thwarted conversion from SAM back to BAM.  Many thanks to Ivan Gregoretti for reporting this bug.  I had never used the BAM output in this way and thus never caught the bug!

src/utils/BamTools/BamWriter.cpp

@@ -243,7 +243,7 @@ void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
     const unsigned int encodedQueryLen = encodedQuery.size();
 
     // store the tag data length
-    const unsigned int tagDataLength = al.TagData.size() + 1;
+    const unsigned int tagDataLength = al.TagData.size();
 
     // assign the BAM core data
     unsigned int buffer[8];

src/utils/version/version.h

@@ -3,6 +3,6 @@
 
 // define the version.  All tools in the 
 // suite carry the same version number.
-#define VERSION "2.5.3"
+#define VERSION "2.5.4"
 
 #endif /* VERSION_H */