* samtools-0.1.5-31 (r448)

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 983c08e6411623da1e322fd071859be4a0af5c3a..f68f400ab5cd086dc88a33e14899abe6cd4e53bb 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -78,6 +78,10 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                                                int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
                                                if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
                                                else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
+                                               if (op_next == BAM_CDEL || op_next == BAM_CINS) {
+                                                       if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK;
+                                                       else p->is_tail = 1;
+                                               }
                                                if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
                                                        p->is_tail = 1; // tail
                                        } else p->is_tail = 1; // this is the last operation; set tail