uint32_t *cigar = bam1_cigar(b);
n2 = 0;
if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
- // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+ // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
r_tid = b->core.tid;
unpad_seq(b, &r);
if (h->target_len[r_tid] != r.l) {
return -1;
} else if (b->core.tid == r_tid) {
; // good case, reference available
+ //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
} else if (fai) {
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]);
if (cigar2[i]) cigar2[k++] = cigar2[i];
n2 = k;
replace_cigar(b, n2, cigar2);
- b->core.pos = posmap[b->core.pos];
}
+ /* 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)));
samwrite(out, b);
}
if (read_ret < -1) {
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;
}
fprintf(stderr, " -S input is SAM (default is BAM)\n");
fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
- fprintf(stderr, " -T FILE reference sequence file [null]\n");
+ fprintf(stderr, " -T FILE padded reference sequence file [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -? longer help\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes:\n\
\n\
1. Requires embedded reference sequences (before the reads for that reference),\n\
- with the future aim to also support a FASTA padded reference sequence file.\n\
+ or ideally a FASTA file of the padded reference sequences (via the -T argument).\n\
\n\
2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
\n");