int op, ol;
op = bam_cigar_op(cigar[k]);
ol = bam_cigar_oplen(cigar[k]);
- assert(op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CSOFT_CLIP);
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
++j;
} else if (op == BAM_CSOFT_CLIP) {
j += ol;
- } else {
+ } else if (op == BAM_CDEL || op == BAM_CPAD) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+ } else {
+ fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ assert(-1);
}
}
}
bam_header_t *h;
bam1_t *b;
kstring_t r, q;
+ int r_tid = -1;
uint32_t *cigar2 = 0;
int n2 = 0, m2 = 0, *posmap = 0;
h = bam_header_read(in);
+ /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
bam_header_write(out, h);
b = bam_init1();
r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
n2 = 0;
if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
int i, k;
+ /*
+ fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+ */
+ r_tid = b->core.tid;
unpad_seq(b, &r);
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap[i] = k; // note that a read should NOT start at a padding
if (r.s[i]) ++k;
}
- } else {
+ } else if (b->core.n_cigar > 0) {
int i, k, op;
+ if (b->core.tid < 0) {
+ fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
+ return -1;
+ } else if (b->core.tid != r_tid) {
+ fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
+ return -1;
+ }
unpad_seq(b, &q);
if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
int main_pad2unpad(int argc, char *argv[])
{
bamFile in, out;
+ int result=0;
if (argc == 1) {
fprintf(stderr, "Usage: samtools depad <in.bam>\n");
return 1;
}
in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
out = bam_dopen(fileno(stdout), "w");
- bam_pad2unpad(in, out);
+ result = bam_pad2unpad(in, out);
bam_close(in); bam_close(out);
- return 0;
+ return result;
}