Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/hgTracks/bamTrack.c	24 Jun 2009 20:33:03 -0000	1.1
+++ src/hg/hgTracks/bamTrack.c	24 Jun 2009 23:57:05 -0000	1.2
@@ -92,8 +92,10 @@
 char *qSeq = needMem(core->l_qseq + 1);
 int i;
 for (i = 0; i < core->l_qseq; i++)
     qSeq[i] = bam_nt16_rev_table[bam1_seqi(s, i)];
+if (lf->orientation == -1)
+    reverseComplement(qSeq, core->l_qseq);
 lf->extra = qSeq;
 slAddHead(&(tg->items), lf);
 return 0;
 }

