src/hg/inc/bamFile.h 1.15

1.15 2010/03/03 19:30:01 angie
Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.

Index: src/hg/inc/bamFile.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/bamFile.h,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/hg/inc/bamFile.h	13 Feb 2010 00:18:38 -0000	1.14
+++ src/hg/inc/bamFile.h	3 Mar 2010 19:30:01 -0000	1.15
@@ -72,10 +72,11 @@
 /* Tally up the alignment's length on the reference sequence from
  * bam's packed-int CIGAR representation. */
 
 struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset,
-			 boolean useStrand);
-/* Convert from bam to ffAli format. */
+			 boolean useStrand, char **retQSeq);
+/* Convert from bam to ffAli format.  If retQSeq is non-null, set it to the 
+ * query sequence into which ffAli needle pointers point. */
 
 bam1_t *bamClone(const bam1_t *bam);
 /* Return a newly allocated copy of bam. */