+ /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */
+ if (b->core.pos != -1) b->core.pos = posmap[b->core.pos];
+ if (b->core.mtid < 0 || b->core.mpos < 0) {
+ /* Nice case, no mate to worry about*/
+ // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+ /* TODO - Warning if FLAG says mate should be mapped? */
+ /* Clean up funny input where mate position is given but mate reference is missing: */
+ b->core.mtid = -1;
+ b->core.mpos = -1;
+ } else if (b->core.mtid == b->core.tid) {
+ /* Nice case, same reference */
+ // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+ b->core.mpos = posmap[b->core.mpos];
+ } else {
+ /* Nasty case, Must load alternative posmap */
+ // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+ if (!fai) {
+ fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+ return -1;
+ }
+ /* Temporarily load the other reference sequence */
+ if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+ fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ b->core.mpos = posmap[b->core.mpos];
+ /* Restore the reference and posmap*/
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+ fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ }
+ /* Most reads will have been moved so safest to always recalculate the BIN value */
+ b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));