X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam2bcf_indel.c;h=5142b3e100aa96a7ab598a95b9953aa4c6034289;hp=2fdee9f75a2261266912b7fe355e9ea51892ff6d;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b301e959d73eee0955c57004f344f17af00703f4

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2fdee9f..5142b3e 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -66,7 +66,7 @@ static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos,
 	for (k = 0; k < c->n_cigar; ++k) {
 		int op = cigar[k] & BAM_CIGAR_MASK;
 		int l = cigar[k] >> BAM_CIGAR_SHIFT;
-		if (op == BAM_CMATCH) {
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 			if (c->pos > tpos) return y;
 			if (x + l > tpos) {
 				*_tpos = tpos;
@@ -222,7 +222,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				for (k = 0; k < b->core.n_cigar; ++k) {
 					int op = cigar[k]&0xf;
 					int j, l = cigar[k]>>4;
-					if (op == BAM_CMATCH) {
+					if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 						for (j = 0; j < l; ++j)
 							if (x + j >= left && x + j < right)
 								cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;