Imported Upstream version 0.1.18

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 5fac17df6ec27d7cbb04b5600c3ce54d5c06b354..0055e8427667dd95151ea1a1bef5dd14e74e15f1 100644 (file)
--- 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);