static void unpad_seq(bam1_t *b, kstring_t *s)
{
int k, j, i;
+ int length;
uint32_t *cigar = bam1_cigar(b);
uint8_t *seq = bam1_seq(b);
- ks_resize(s, b->core.l_qseq);
+ // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+ // We need the padded length after alignment from the CIGAR (excluding
+ // soft clips S, but including pads from CIGAR D operations)
+ length = 0;
+ for (k = 0; k < b->core.n_cigar; ++k) {
+ int op, ol;
+ op= bam_cigar_op(cigar[k]);
+ ol = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
+ length += ol;
+ }
+ ks_resize(s, length);
for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
int op, ol;
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 || op == BAM_CPAD) {
+ } else if (op == BAM_CHARD_CLIP) {
+ /* do nothing */
+ } else if (op == BAM_CDEL) {
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));
+ fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
assert(-1);
}
}
+ assert(length == s->l);
}
int bam_pad2unpad(bamFile in, bamFile out)
bam_header_t *h;
bam1_t *b;
kstring_t r, q;
- int r_tid = -1;
+ 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;
*/
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 if (b->core.n_cigar > 0) {
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_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ } else 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]);
+ }
+ }
+ /* 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);
+ /* Include any pads if starts with an insert */
+ if (q.s[0] == BAM_CINS) {
+ 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));
+ }
+ /* 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));
} else ++k;
}
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_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ } else 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/X/=/D operators, e.g. 5M2P10M -> 15M */
+ int pre_op, post_op;
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;
+ if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+ pre_op = bam_cigar_op(cigar2[i-2]);
+ post_op = bam_cigar_op(cigar2[i]);
+ /* Note don't need to check for X/= as code above will use M only */
+ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+ /* This is a redundant P operator */
+ cigar2[i-1] = 0; // i.e. 0M
+ /* If had same operator either side, combine them in post_op */
+ if (pre_op == post_op) {
+ /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+ cigar2[i-2] = 0; // i.e. 0M
+ }
+ }
+ }
+ /* Remove the zero'd operators (0M) */
for (i = k = 0; i < n2; ++i)
if (cigar2[i]) cigar2[k++] = cigar2[i];
n2 = k;
projects / samtools.git / blobdiff