Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 55e51e27804cfc58fc5576b40ae7ba10416a3e8f..3e26f74c0e7dac3012ad5805a99d2311e6d274a6 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -79,12 +79,12 @@ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
                is_head = 1;
                if (c->n_cigar == 1) { // just one operation, save a loop
                        if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
-               } else { // find the first match
+               } else { // find the first match or deletion
                        for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
                                int op = _cop(cigar[k]);
                                int l = _cln(cigar[k]);
-                               if (op == BAM_CMATCH) break;
-                               else if (op == BAM_CDEL || op == BAM_CREF_SKIP) s->x += l;
+                               if (op == BAM_CMATCH || op == BAM_CDEL) break;
+                               else if (op == BAM_CREF_SKIP) s->x += l;
                                else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
                        }
                        assert(k < c->n_cigar);