int bam_pad2unpad(bamFile in, bamFile out)
{
bam_header_t *h;
bam1_t *b;
kstring_t r, q;
uint32_t *cigar2 = 0;
int n2 = 0, m2 = 0, *posmap = 0;
h = bam_header_read(in);
bam_header_write(out, h);
b = bam_init1();
r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
while (bam_read1(in, b) >= 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) {
int i, k;
unpad_seq(b, &r);
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
if (r.s[i]) ++k;
}
} else {
int i, k, op;
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)
q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
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));
op = q.s[i]; k = 1;
} 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]);
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;
for (i = k = 0; i < n2; ++i)
if (cigar2[i]) cigar2[k++] = cigar2[i];
n2 = k;
replace_cigar(b, n2, cigar2);
b->core.pos = posmap[b->core.pos];
}
bam_write1(out, b);
}
free(r.s); free(q.s); free(posmap);
bam_destroy1(b);
bam_header_destroy(h);
return 0;
}
int bam_pad2unpad(samFile *in, samFile *out, bam_hdr_t *h, faidx_t *fai)
{
bam1_t *b = 0;
kstring_t r, q;
int r_tid = -1;
uint32_t *cigar2 = 0;
int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
b = bam_init1();
r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
int read_ret;
while ((read_ret = sam_read1(in, h, b)) >= 0) { // read one alignment from `in'
// Cannot depad unmapped CRAM data
if (b->core.flag & BAM_FUNMAP)
goto next_seq;
uint32_t *cigar = bam_get_cigar(b);
n2 = 0;
if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam_get_qname(b), h->target_name[b->core.tid]) == 0) {
// fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam_get_qname(b));
r_tid = b->core.tid;
if (0!=unpad_seq(b, &r)) {
fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in reference %s\n", bam_get_qname(b));
return -1;
};
if (h->target_len[r_tid] != r.l) {
fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %u in BAM header, but %llu in embedded reference\n", bam_get_qname(b), h->target_len[r_tid], (unsigned long long)(r.l));
return -1;
}
if (fai) {
// Check the embedded reference matches the FASTA file
if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
return -1;
}
assert(r.l == q.l);
int i;
for (i = 0; i < r.l; ++i) {
if (r.s[i] != q.s[i]) {
// Show gaps as ASCII 45
fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
h->target_name[b->core.tid], i+1,
r.s[i] ? seq_nt16_str[(int)r.s[i]] : 45,
q.s[i] ? seq_nt16_str[(int)q.s[i]] : 45);
return -1;
}
}
}
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = update_posmap(posmap, r);
} 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", bam_get_qname(b));
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], bam_get_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]);
return -1;
}
posmap = update_posmap(posmap, r);
r_tid = b->core.tid;
// fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
} else {
fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
return -1;
}
if (0!=unpad_seq(b, &q)) {
fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in read %s\n", bam_get_qname(b));
return -1;
};
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));
k = 0;
} else if (q.s[0] == BAM_CPAD) {
// Join 'k' CPAD to our first cigar op CPAD too.
for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
} else {
k = 0;
}
/* Count consecutive CIGAR operators to turn into a CIGAR string */
for (i = 1, k++, op = q.s[0]; i < q.l; ++i) {
if (op != q.s[i]) {
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
op = q.s[i]; k = 1;
} 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]);
} 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-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;
replace_cigar(b, n2, cigar2);
}
/* 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", bam_get_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", bam_get_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_endpos(b));
next_seq:
sam_write1(out, h, b);
}
if (read_ret < -1) {
fprintf(stderr, "[depad] truncated file.\n");
ret = 1;
}
free(r.s); free(q.s); free(posmap);
bam_destroy1(b);
return ret;
}
