src/hg/inc/bamFile.h 1.3

Index: src/hg/inc/bamFile.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/bamFile.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/inc/bamFile.h	3 Aug 2009 22:00:24 -0000	1.2
+++ src/hg/inc/bamFile.h	3 Aug 2009 22:14:39 -0000	1.3
@@ -32,9 +32,11 @@
 return n;
 }
 
 char *bamGetQuerySequence(const bam1_t *bam);
-/* Return the nucleotide sequence encoded in bam. */
+/* Return the nucleotide sequence encoded in bam.  The BAM format 
+ * reverse-complements query sequence when the alignment is on the - strand,
+ * so here we rev-comp it back to restore the original query sequence. */
 
 char *bamGetCigar(const bam1_t *bam);
 /* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */