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#include <unistd.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include "stdaln.h"
#include "bwase.h"
#include "bwtaln.h"
#include "bntseq.h"
#include "utils.h"
#include "kstring.h"
int g_log_n[256];
char *bwa_rg_line, *bwa_rg_id;
void bwa_print_sam_PG();
void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
{
int i, cnt, best;
if (n_aln == 0) {
s->type = BWA_TYPE_NO_MATCH;
s->c1 = s->c2 = 0;
return;
}
if (set_main) {
best = aln[0].score;
for (i = cnt = 0; i < n_aln; ++i) {
const bwt_aln1_t *p = aln + i;
if (p->score > best) break;
if (drand48() * (p->l - p->k + 1 + cnt) > (double)cnt) {
s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape; s->strand = p->a;
s->score = p->score;
s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
}
cnt += p->l - p->k + 1;
}
s->c1 = cnt;
for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
s->c2 = cnt - s->c1;
s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
}
if (n_multi) {
int k, rest, n_occ, z = 0;
for (k = n_occ = 0; k < n_aln; ++k) {
const bwt_aln1_t *q = aln + k;
n_occ += q->l - q->k + 1;
}
if (s->multi) free(s->multi);
if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
s->multi = 0; s->n_multi = 0;
return;
}
/* The following code is more flexible than what is required
* here. In principle, due to the requirement above, we can
* simply output all hits, but the following samples "rest"
* number of random hits. */
rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
s->multi = calloc(rest, sizeof(bwt_multi1_t));
for (k = 0; k < n_aln; ++k) {
const bwt_aln1_t *q = aln + k;
if (q->l - q->k + 1 <= rest) {
bwtint_t l;
for (l = q->k; l <= q->l; ++l) {
s->multi[z].pos = l;
s->multi[z].gap = q->n_gapo + q->n_gape;
s->multi[z].mm = q->n_mm;
s->multi[z++].strand = q->a;
}
rest -= q->l - q->k + 1;
} else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here.
int j, i, k;
for (j = rest, i = q->l - q->k + 1, k = 0; j > 0; --j) {
double p = 1.0, x = drand48();
while (x < p) p -= p * j / (i--);
s->multi[z].pos = q->l - i;
s->multi[z].gap = q->n_gapo + q->n_gape;
s->multi[z].mm = q->n_mm;
s->multi[z++].strand = q->a;
}
rest = 0;
break;
}
}
s->n_multi = z;
for (k = z = 0; k < s->n_multi; ++k)
if (s->multi[k].pos != s->sa)
s->multi[z++] = s->multi[k];
s->n_multi = z < n_multi? z : n_multi;
}
}
void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
{
bwa_aln2seq_core(n_aln, aln, s, 1, 0);
}
int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
{
int n;
if (p->c1 == 0) return 23;
if (p->c1 > 1) return 0;
if (p->n_mm == mm) return 25;
if (p->c2 == 0) return 37;
n = (p->c2 >= 255)? 255 : p->c2;
return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
}
/**
* Derive the actual position in the read from the given suffix array
* coordinates. Note that the position will be approximate based on
* whether indels appear in the read and whether calculations are
* performed from the start or end of the read.
*/
void bwa_cal_pac_pos_core(const bwt_t *forward_bwt, const bwt_t *reverse_bwt, bwa_seq_t *seq, const int max_mm, const float fnr)
{
int max_diff;
if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) return;
max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
if (seq->strand) { // reverse strand only
seq->pos = bwt_sa(forward_bwt, seq->sa);
seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
} else { // forward strand only
/* NB: For gapped alignment, p->pos may not be correct, which
* will be fixed in refine_gapped_core(). This line also
* determines the way "x" is calculated in
* refine_gapped_core() when (ext < 0 && is_end == 0). */
seq->pos = reverse_bwt->seq_len - (bwt_sa(reverse_bwt, seq->sa) + seq->len);
seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
}
}
void bwa_cal_pac_pos(const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
{
int i, j;
char str[1024];
bwt_t *bwt;
// load forward SA
strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
for (i = 0; i != n_seqs; ++i) {
if (seqs[i].strand) bwa_cal_pac_pos_core(bwt, 0, &seqs[i], max_mm, fnr);
for (j = 0; j < seqs[i].n_multi; ++j) {
bwt_multi1_t *p = seqs[i].multi + j;
if (p->strand) p->pos = bwt_sa(bwt, p->pos);
}
}
bwt_destroy(bwt);
// load reverse BWT and SA
strcpy(str, prefix); strcat(str, ".rbwt"); bwt = bwt_restore_bwt(str);
strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str, bwt);
for (i = 0; i != n_seqs; ++i) {
if (!seqs[i].strand) bwa_cal_pac_pos_core(0, bwt, &seqs[i], max_mm, fnr);
for (j = 0; j < seqs[i].n_multi; ++j) {
bwt_multi1_t *p = seqs[i].multi + j;
if (!p->strand) p->pos = bwt->seq_len - (bwt_sa(bwt, p->pos) + seqs[i].len);
}
}
bwt_destroy(bwt);
}
/* is_end_correct == 1 if (*pos+len) gives the correct coordinate on
* forward strand. This happens when p->pos is calculated by
* bwa_cal_pac_pos(). is_end_correct==0 if (*pos) gives the correct
* coordinate. This happens only for color-converted alignment. */
static bwa_cigar_t *refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, bwtint_t *_pos,
int ext, int *n_cigar, int is_end_correct)
{
bwa_cigar_t *cigar = 0;
ubyte_t *ref_seq;
int l = 0, path_len, ref_len;
AlnParam ap = aln_param_bwa;
path_t *path;
int64_t k, __pos = *_pos > l_pac? (int64_t)((int32_t)*_pos) : *_pos;
ref_len = len + abs(ext);
if (ext > 0) {
ref_seq = (ubyte_t*)calloc(ref_len, 1);
for (k = __pos; k < __pos + ref_len && k < l_pac; ++k)
ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
} else {
int64_t x = __pos + (is_end_correct? len : ref_len);
ref_seq = (ubyte_t*)calloc(ref_len, 1);
for (l = 0, k = x - ref_len > 0? x - ref_len : 0; k < x && k < l_pac; ++k)
ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
}
path = (path_t*)calloc(l+len, sizeof(path_t));
aln_global_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len);
cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
if (ext < 0 && is_end_correct) { // fix coordinate for reads mapped on the forward strand
for (l = k = 0; k < *n_cigar; ++k) {
if (__cigar_op(cigar[k]) == FROM_D) l -= __cigar_len(cigar[k]);
else if (__cigar_op(cigar[k]) == FROM_I) l += __cigar_len(cigar[k]);
}
__pos += l;
}
if (__cigar_op(cigar[0]) == FROM_D) { // deletion at the 5'-end
__pos += __cigar_len(cigar[0]);
for (k = 0; k < *n_cigar - 1; ++k) cigar[k] = cigar[k+1];
--(*n_cigar);
}
if (__cigar_op(cigar[*n_cigar-1]) == FROM_D) --(*n_cigar); // deletion at the 3'-end
// change "I" at either end of the read to S. just in case. This should rarely happen...
if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(3, (__cigar_len(cigar[*n_cigar-1])));
if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
*_pos = (bwtint_t)__pos;
free(ref_seq); free(path);
return cigar;
}
char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
{
bwtint_t x, y;
int z, u, c, nm = 0;
str->l = 0; // reset
x = pos; y = 0;
if (cigar) {
int k, l;
for (k = u = 0; k < n_cigar; ++k) {
l = __cigar_len(cigar[k]);
if (__cigar_op(cigar[k]) == FROM_M) {
for (z = 0; z < l && x+z < l_pac; ++z) {
c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
ksprintf(str, "%d", u);
kputc("ACGTN"[c], str);
++nm;
u = 0;
} else ++u;
}
x += l; y += l;
/* } else if (cigar[k]>>14 == FROM_I || cigar[k]>>14 == 3) { */
} else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
y += l;
if (__cigar_op(cigar[k]) == FROM_I) nm += l;
} else if (__cigar_op(cigar[k]) == FROM_D) {
ksprintf(str, "%d", u);
kputc('^', str);
for (z = 0; z < l && x+z < l_pac; ++z)
kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
u = 0;
x += l; nm += l;
}
}
} else { // no gaps
for (z = u = 0; z < (bwtint_t)len; ++z) {
c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
ksprintf(str, "%d", u);
kputc("ACGTN"[c], str);
++nm;
u = 0;
} else ++u;
}
}
ksprintf(str, "%d", u);
*_nm = nm;
return strdup(str->s);
}
void bwa_correct_trimmed(bwa_seq_t *s)
{
if (s->len == s->full_len) return;
if (s->strand == 0) { // forward
if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
s->cigar[s->n_cigar-1] += s->full_len - s->len;
} else {
if (s->cigar == 0) {
s->n_cigar = 2;
s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
s->cigar[0] = __cigar_create(0, s->len);
} else {
++s->n_cigar;
s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
}
s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
}
} else { // reverse
if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
s->cigar[0] += s->full_len - s->len;
} else {
if (s->cigar == 0) {
s->n_cigar = 2;
s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
s->cigar[1] = __cigar_create(0, s->len);
} else {
++s->n_cigar;
s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
}
s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
}
}
s->len = s->full_len;
}
void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns)
{
ubyte_t *pacseq, *ntpac = 0;
int i, j;
kstring_t *str;
if (ntbns) { // in color space
ntpac = (ubyte_t*)calloc(ntbns->l_pac/4+1, 1);
rewind(ntbns->fp_pac);
fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac);
}
if (!_pacseq) {
pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
rewind(bns->fp_pac);
fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
} else pacseq = _pacseq;
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *s = seqs + i;
seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap == 0) continue;
q->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
(q->strand? 1 : -1) * q->gap, &n_cigar, 1);
q->n_cigar = n_cigar;
}
if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
s->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
(s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 1);
}
if (ntbns) { // in color space
for (i = 0; i < n_seqs; ++i) {
bwa_seq_t *s = seqs + i;
bwa_cs2nt_core(s, bns->l_pac, ntpac);
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap == 0) continue;
free(q->cigar);
q->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
(q->strand? 1 : -1) * q->gap, &n_cigar, 0);
q->n_cigar = n_cigar;
}
if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
free(s->cigar);
s->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
(s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 0);
}
}
}
// generate MD tag
str = (kstring_t*)calloc(1, sizeof(kstring_t));
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *s = seqs + i;
if (s->type != BWA_TYPE_NO_MATCH) {
int nm;
s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
bns->l_pac, ntbns? ntpac : pacseq, str, &nm);
s->nm = nm;
}
}
free(str->s); free(str);
// correct for trimmed reads
if (!ntbns) // trimming is only enabled for Illumina reads
for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
if (!_pacseq) free(pacseq);
free(ntpac);
}
int64_t pos_end(const bwa_seq_t *p)
{
if (p->cigar) {
int j;
int64_t x = p->pos;
for (j = 0; j != p->n_cigar; ++j) {
int op = __cigar_op(p->cigar[j]);
if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
}
return x;
} else return p->pos + p->len;
}
int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
{
if (p->cigar) {
int j;
int64_t x = p->pos;
for (j = 0; j != p->n_cigar; ++j) {
int op = __cigar_op(p->cigar[j]);
if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
}
return x;
} else return p->pos + len;
}
static int64_t pos_5(const bwa_seq_t *p)
{
if (p->type != BWA_TYPE_NO_MATCH)
return p->strand? pos_end(p) : p->pos;
return -1;
}
void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
{
int j;
if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
int seqid, nn, am = 0, flag = p->extra_flag;
char XT;
if (p->type == BWA_TYPE_NO_MATCH) {
p->pos = mate->pos;
p->strand = mate->strand;
flag |= SAM_FSU;
j = 1;
} else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
// get seqid
nn = bns_coor_pac2real(bns, p->pos, j, &seqid);
if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
// update flag and print it
if (p->strand) flag |= SAM_FSR;
if (mate) {
if (mate->type != BWA_TYPE_NO_MATCH) {
if (mate->strand) flag |= SAM_FMR;
} else flag |= SAM_FMU;
}
err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
// print CIGAR
if (p->cigar) {
for (j = 0; j != p->n_cigar; ++j)
err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
} else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
else err_printf("%dM", p->len);
// print mate coordinate
if (mate && mate->type != BWA_TYPE_NO_MATCH) {
int m_seqid, m_is_N;
long long isize;
am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
// redundant calculation here, but should not matter too much
m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
} else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
else err_printf("\t*\t0\t0\t");
// print sequence and quality
if (p->strand == 0)
for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
putchar('\t');
if (p->qual) {
if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
err_printf("%s", p->qual);
} else err_printf("*");
if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
if (p->type != BWA_TYPE_NO_MATCH) {
int i;
// calculate XT tag
XT = "NURM"[p->type];
if (nn > 10) XT = 'N';
// print tags
err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
if (nn) err_printf("\tXN:i:%d", nn);
if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
err_printf("\tX0:i:%d", p->c1);
if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
}
err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
if (p->md) err_printf("\tMD:Z:%s", p->md);
// print multiple hits
if (p->n_multi) {
err_printf("\tXA:Z:");
for (i = 0; i < p->n_multi; ++i) {
bwt_multi1_t *q = p->multi + i;
int k;
j = pos_end_multi(q, p->len) - q->pos;
nn = bns_coor_pac2real(bns, q->pos, j, &seqid);
err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
(int)(q->pos - bns->anns[seqid].offset + 1));
if (q->cigar) {
for (k = 0; k < q->n_cigar; ++k)
err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
} else err_printf("%dM", p->len);
err_printf(",%d;", q->gap + q->mm);
}
}
}
putchar('\n');
} else { // this read has no match
ubyte_t *s = p->strand? p->rseq : p->seq;
int flag = p->extra_flag | SAM_FSU;
if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
putchar('\t');
if (p->qual) {
if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
err_printf("%s", p->qual);
} else err_printf("*");
if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
putchar('\n');
}
}
bntseq_t *bwa_open_nt(const char *prefix)
{
bntseq_t *ntbns;
char *str;
str = (char*)calloc(strlen(prefix) + 10, 1);
strcat(strcpy(str, prefix), ".nt");
ntbns = bns_restore(str);
free(str);
return ntbns;
}
void bwa_print_sam_SQ(const bntseq_t *bns)
{
int i;
for (i = 0; i < bns->n_seqs; ++i)
err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
if (bwa_rg_line) err_printf("%s\n", bwa_rg_line);
}
void bwase_initialize()
{
int i;
for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
}
char *bwa_escape(char *s)
{
char *p, *q;
for (p = q = s; *p; ++p) {
if (*p == '\\') {
++p;
if (*p == 't') *q++ = '\t';
else if (*p == 'n') *q++ = '\n';
else if (*p == 'r') *q++ = '\r';
else if (*p == '\\') *q++ = '\\';
} else *q++ = *p;
}
*q = '\0';
return s;
}
int bwa_set_rg(const char *s)
{
char *p, *q, *r;
if (strstr(s, "@RG") != s) return -1;
if (bwa_rg_line) free(bwa_rg_line);
if (bwa_rg_id) free(bwa_rg_id);
bwa_rg_line = strdup(s);
bwa_rg_id = 0;
bwa_escape(bwa_rg_line);
p = strstr(bwa_rg_line, "\tID:");
if (p == 0) return -1;
p += 4;
for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
bwa_rg_id = calloc(q - p + 1, 1);
for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
*r++ = *q;
return 0;
}
void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
{
extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
int i, n_seqs, tot_seqs = 0, m_aln;
bwt_aln1_t *aln = 0;
bwa_seq_t *seqs;
bwa_seqio_t *ks;
clock_t t;
bntseq_t *bns, *ntbns = 0;
FILE *fp_sa;
gap_opt_t opt;
// initialization
bwase_initialize();
bns = bns_restore(prefix);
srand48(bns->seed);
fp_sa = xopen(fn_sa, "r");
m_aln = 0;
fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
ntbns = bwa_open_nt(prefix);
bwa_print_sam_SQ(bns);
bwa_print_sam_PG();
// set ks
ks = bwa_open_reads(opt.mode, fn_fa);
// core loop
while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode, opt.trim_qual)) != 0) {
tot_seqs += n_seqs;
t = clock();
// read alignment
for (i = 0; i < n_seqs; ++i) {
bwa_seq_t *p = seqs + i;
int n_aln;
fread(&n_aln, 4, 1, fp_sa);
if (n_aln > m_aln) {
m_aln = n_aln;
aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
}
fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
}
fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
bwa_cal_pac_pos(prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
bwa_refine_gapped(bns, n_seqs, seqs, 0, ntbns);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
fprintf(stderr, "[bwa_aln_core] print alignments... ");
for (i = 0; i < n_seqs; ++i)
bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
bwa_free_read_seq(n_seqs, seqs);
fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
}
// destroy
bwa_seq_close(ks);
if (ntbns) bns_destroy(ntbns);
bns_destroy(bns);
fclose(fp_sa);
free(aln);
}
int bwa_sai2sam_se(int argc, char *argv[])
{
int c, n_occ = 3;
while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
switch (c) {
case 'h': break;
case 'r':
if (bwa_set_rg(optarg) < 0) {
fprintf(stderr, "[%s] malformated @RG line\n", __func__);
return 1;
}
break;
case 'n': n_occ = atoi(optarg); break;
case 'f': xreopen(optarg, "w", stdout); break;
default: return 1;
}
}
if (optind + 3 > argc) {
fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
return 1;
}
bwa_sai2sam_se_core(argv[optind], argv[optind+1], argv[optind+2], n_occ);
free(bwa_rg_line); free(bwa_rg_id);
return 0;
}