n2 = k;
replace_cigar(b, n2, cigar2);
b->core.pos = posmap[b->core.pos];
+ if (b->core.mpos < 0) {
+ /* Nice case, no mate to worry about*/
+ } else if (b->core.mtid == b->core.tid) {
+ /* Nice case, same reference */
+ b->core.mpos = posmap[b->core.mpos];
+ } else {
+ /* Nasty case, Must load alternative posmap */
+ 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);
+ }
}
samwrite(out, b);
}
if (strlen(header->text) < header->l_text) {
//fprintf(stderr, "[depad] Reallocating header buffer\n");
assert (newtext == header->text);
- newtext = calloc(strlen(header->text) + 1, 1);
+ newtext = malloc(strlen(header->text) + 1);
strcpy(newtext, header->text);
free(header->text);
header->text = newtext;
depad_end:
// close files, free and return
- free(fn_list); free(fn_out);
- if (h != in->header) bam_header_destroy(h);
+ if (fai) fai_destroy(fai);
+ if (h != in->header) bam_header_destroy(h);
samclose(in);
samclose(out);
- fai_destroy(fai);
+ free(fn_list); free(fn_out);
return ret;
}