op = bam_cigar_op(cigar[k]);
ol = bam_cigar_oplen(cigar[k]);
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;
+ for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
} else if (op == BAM_CSOFT_CLIP) {
j += ol;
- } else if (op == BAM_CDEL) {
+ } else if (op == BAM_CHARD_CLIP) {
+ /* do nothing */
+ } else if (op == BAM_CDEL || op == BAM_CPAD) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
} else {
- fprintf(stderr, "[unpad_seq] Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %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);
+ if (h->target_len[r_tid] != r.l) {
+ fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ return -1;
+ }
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = realloc(posmap, r.m * sizeof(int));
for (i = k = 0; i < r.l; ++i) {
- posmap[i] = k; // note that a read should NOT start at a padding
+ posmap[i] = k;
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]);
+ if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[1]);
+ }
+ }
+ /* Include any pads if starts with an insert */
+ for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+ if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+ /* Determine CIGAR operator for each base in the aligned read */
for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+ /* Count consecutive CIGAR operators to turn into a CIGAR string */
for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
if (op != q.s[i]) {
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
}
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+ if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+ }
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ }
+ /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
for (i = 2; i < n2; ++i)
if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
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;
}