X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam.c.pysam.c;fp=samtools%2Fbam.c.pysam.c;h=ad263395de51eb3b38d56ffdcd9041a8dac1864e;hp=28cdbd74b0d751246c6726f5f88a1499eb87a30f;hb=36e29386e0547c68f3468c92781c67cf5e180903;hpb=3af2785da461666b27cc5b71e36ccd8deb7532fb

diff --git a/samtools/bam.c.pysam.c b/samtools/bam.c.pysam.c
index 28cdbd7..ad26339 100644
--- a/samtools/bam.c.pysam.c
+++ b/samtools/bam.c.pysam.c
@@ -34,7 +34,7 @@ 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;
@@ -270,7 +270,7 @@ 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);