src/hg/hgTracks/bamTrack.c 1.25

Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 4 -r1.24 -r1.25
--- src/hg/hgTracks/bamTrack.c	14 Jan 2010 07:39:19 -0000	1.24
+++ src/hg/hgTracks/bamTrack.c	13 Feb 2010 00:18:39 -0000	1.25
@@ -50,16 +50,16 @@
 	    slAddHead(&sfList, sf);
 	    tLength += n;
 	    break;
 	case 'I': // inserted in query
-	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	    qPos += n;
 	    break;
 	case 'D': // deleted from query
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    tPos += n;
 	    tLength += n;
 	    break;
+	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
 	case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
 	    break;
 	default:
@@ -138,8 +138,10 @@
 lf->components = sfFromNumericCigar(bam, &length);
 lf->start = lf->tallStart = core->pos;
 lf->end = lf->tallEnd = core->pos + length;
 lf->extra = bamGetQuerySequence(bam, TRUE);
+int clippedQLen;
+bamGetSoftClipping(bam, NULL, NULL, &clippedQLen);
 if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
     sameString(btd->grayMode, BAM_GRAY_MODE_ALI_QUAL))
     {
     // hardcode min & max for now; if user demand, make into tdb/cart vars.
@@ -148,9 +150,9 @@
 else if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
 	 sameString(btd->grayMode, BAM_GRAY_MODE_BASE_QUAL))
     {
     UBYTE *quals = bamGetQueryQuals(bam, TRUE);
-    lf->components = expandSfQuals(lf->components, quals, lf->orientation, core->l_qseq);
+    lf->components = expandSfQuals(lf->components, quals, lf->orientation, clippedQLen);
     lf->grayIx = maxShade - 3;
     }
 else if (sameString(btd->colorMode, BAM_COLOR_MODE_TAG) && isNotEmpty(btd->userTag))
     {