X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_pileup.c;h=a49f795d73d4f0ed1ad3a9592108f3be2a917579;hb=6ee6fd65332260af63fbfbf0a625ea3847371eda;hp=62d5fa1d2b3d9b2171b98eccb9f583755e379822;hpb=253dbf083d8a84721ae6ac63af786c8dcf566ecb;p=samtools.git

diff --git a/bam_pileup.c b/bam_pileup.c
index 62d5fa1..a49f795 100644
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -114,22 +114,25 @@ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
 	}
 	{ // collect pileup information
 		int op, l;
-		op = _cop(cigar[s->k]);
-		l = _cln(cigar[s->k]);
+		op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
 		p->is_del = p->indel = p->is_refskip = 0;
-		if (op == BAM_CMATCH) {
-			p->qpos = s->y + (pos - s->x);
-			if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
-				int op2 = _cop(cigar[s->k+1]);
-				int l2 = _cln(cigar[s->k+1]);
-				if (op2 == BAM_CDEL) p->indel = -(int)l2;
-				else if (op2 == BAM_CINS) p->indel = l2;
-				else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
-					op2 = _cop(cigar[s->k+2]); l2 = _cln(cigar[s->k+2]);
-					if (op2 == BAM_CDEL) p->indel = -(int)l2;
-					else if (op2 == BAM_CINS) p->indel = l2;
+		if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
+			int op2 = _cop(cigar[s->k+1]);
+			int l2 = _cln(cigar[s->k+1]);
+			if (op2 == BAM_CDEL) p->indel = -(int)l2;
+			else if (op2 == BAM_CINS) p->indel = l2;
+			else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
+				int l3 = 0;
+				for (k = s->k + 2; k < c->n_cigar; ++k) {
+					op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
+					if (op2 == BAM_CINS) l3 += l2;
+					else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP) break;
 				}
+				if (l3 > 0) p->indel = l3;
 			}
+		}
+		if (op == BAM_CMATCH) {
+			p->qpos = s->y + (pos - s->x);
 		} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
 			p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
 			p->is_refskip = (op == BAM_CREF_SKIP);