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) {
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) {
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = update_posmap(posmap, r);
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = update_posmap(posmap, r);
return -1;
} else if (b->core.tid == r_tid) {
; // good case, reference available
return -1;
} else if (b->core.tid == r_tid) {
; // good case, reference available
} 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]);
} 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]);
n2 = k;
replace_cigar(b, n2, cigar2);
b->core.pos = posmap[b->core.pos];
n2 = k;
replace_cigar(b, n2, cigar2);
b->core.pos = posmap[b->core.pos];
+ // 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 */
} 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 */
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;
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;