Imported Upstream version 0.1.7~dfsg

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 3ffd52851e3be64bed628081b2b57d8ca6378b8b..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
@@ -166,9 +170,13 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
                if (b->core.flag & buf->flag_mask) return 0;
                bam_copy1(&buf->tail->b, b);
                buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b));
-               if (!(b->core.tid >= buf->max_tid || (b->core.tid == buf->max_tid && buf->tail->beg >= buf->max_pos))) {
-                       fprintf(stderr, "[bam_pileup_core] the input is not sorted. Abort!\n");
-                       abort();
+               if (b->core.tid < buf->max_tid) {
+                       fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+                       return -1;
+               }
+               if ((b->core.tid == buf->max_tid) && (buf->tail->beg < buf->max_pos)) {
+                       fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+                       return -1;
                }
                buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg;
                if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) {
@@ -212,3 +220,19 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
        }
        return 0;
 }
+
+int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
+{
+       bam_plbuf_t *buf;
+       int ret;
+       bam1_t *b;
+       b = bam_init1();
+       buf = bam_plbuf_init(func, func_data);
+       bam_plbuf_set_mask(buf, mask);
+       while ((ret = bam_read1(fp, b)) >= 0)
+               bam_plbuf_push(b, buf);
+       bam_plbuf_push(0, buf);
+       bam_plbuf_destroy(buf);
+       bam_destroy1(b);
+       return 0;
+}