src/hg/hgc/bamClick.c 1.15

Index: src/hg/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/hg/hgc/bamClick.c	11 Jan 2010 18:34:25 -0000	1.14
+++ src/hg/hgc/bamClick.c	13 Feb 2010 00:18:39 -0000	1.15
@@ -41,9 +41,13 @@
 bamShowTags(bam);
 puts("<BR>");
 printf("<B>Flags: </B><tt>0x%02x:</tt><BR>\n &nbsp;&nbsp;", core->flag);
 bamShowFlagsEnglish(bam);
-puts("<BR><BR>");
+puts("<BR>");
+if (bamIsRc(bam))
+    printf("<em>Note: although the read was mapped to the reverse strand of the genome, "
+	   "the sequence and CIGAR in BAM are relative to the forward strand.</em><BR>\n");
+puts("<BR>");
 char nibName[HDB_MAX_PATH_STRING];
 hNibForChrom(database, seqName, nibName);
 struct dnaSeq *genoSeq = hFetchSeq(nibName, seqName, tStart, tEnd);
 struct ffAli *ffa = bamToFfAli(bam, genoSeq, tStart, useStrand);
@@ -53,10 +57,12 @@
 ffShowSideBySide(stdout, ffa, qSeq, 0, genoSeq->dna, tStart, tLength, 0, tLength, 8, isRc,
 		 FALSE);
 printf("<B>Sequence quality scores:</B><BR>\n<TT><TABLE><TR>\n");
 UBYTE *quals = bamGetQueryQuals(bam, useStrand);
+int clippedQLen;
+bamGetSoftClipping(bam, NULL, NULL, &clippedQLen);
 int i;
-for (i = 0;  i < core->l_qseq;  i++)
+for (i = 0;  i < clippedQLen;  i++)
     {
     if (i > 0 && (i % 24) == 0)
 	printf("</TR>\n<TR>");
     printf("<TD>%c<BR>%d</TD>", qSeq[i], quals[i]);