X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=0055e8427667dd95151ea1a1bef5dd14e74e15f1;hp=5fac17df6ec27d7cbb04b5600c3ce54d5c06b354;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b301e959d73eee0955c57004f344f17af00703f4

diff --git a/bam.c b/bam.c
index 5fac17d..0055e84 100644
--- a/bam.c
+++ b/bam.c
@@ -32,7 +32,7 @@ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
 	int32_t l = 0;
 	for (k = 0; k < c->n_cigar; ++k) {
 		int op = cigar[k] & BAM_CIGAR_MASK;
-		if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+		if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
 			l += cigar[k] >> BAM_CIGAR_SHIFT;
 	}
 	return l;
@@ -268,7 +268,7 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 	else {
 		for (i = 0; i < c->n_cigar; ++i) {
 			kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
-			kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+			kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
 		}
 	}
 	kputc('\t', &str);