int bam_plp_push(bam_plp_t iter, const bam1_t *b)
{
if (iter->error) return -1;
if (b) {
if (b->core.tid < 0) return 0;
if (b->core.flag & iter->flag_mask) return 0;
if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
bam_copy1(&iter->tail->b, b);
iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
if (b->core.tid < iter->max_tid) {
fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
iter->error = 1;
return -1;
}
if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
iter->error = 1;
return -1;
}
iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
iter->tail->next = mp_alloc(iter->mp);
iter->tail = iter->tail->next;
}
} else iter->is_eof = 1;
return 0;
}
GtSamAlignment *gt_sam_alignment_clone(GtSamAlignment *sam_alignment)
{
GtSamAlignment *clone;
gt_assert(sam_alignment != NULL);
clone = gt_sam_alignment_new(sam_alignment->alphabet);
(void)bam_copy1(clone->s_alignment, sam_alignment->s_alignment);
clone->rightmost = sam_alignment->rightmost;
return clone;
}
