src/hg/hgc/bamClick.c 1.10

Index: src/hg/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 4 -r1.9 -r1.10
--- src/hg/hgc/bamClick.c	23 Sep 2009 23:50:30 -0000	1.9
+++ src/hg/hgc/bamClick.c	24 Sep 2009 04:33:50 -0000	1.10
@@ -46,9 +46,18 @@
 printf("<B>Alignment of %s to %s:%d-%d%s:</B><BR>\n", itemName,
        seqName, tStart+1, tEnd, (isRc ? " (reverse complemented)" : ""));
 ffShowSideBySide(stdout, ffa, qSeq, 0, genoSeq->dna, tStart, tLength, 0, tLength, 8, isRc,
 		 FALSE);
-//TODO: show flags properly, maybe display sequence quality scores
+printf("<B>Sequence quality scores:</B><BR>\n<TT><TABLE><TR>\n");
+UBYTE *quals = bamGetQueryQuals(bam);
+int i;
+for (i = 0;  i < core->l_qseq;  i++)
+    {
+    if (i > 0 && (i % 24) == 0)
+	printf("</TR>\n<TR>");
+    printf("<TD>%c<BR>%d</TD>", qSeq[i], quals[i]);
+    }
+printf("</TR></TABLE></TT>\n");
 }
 
 static void showOverlap(const bam1_t *leftBam, const bam1_t *rightBam)
 /* If the two reads overlap, show how. */