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fast-bwa/bwase.c

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#include <unistd.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <assert.h>
#include "bwase.h"
#include "bwtaln.h"
#include "bntseq.h"
#include "utils.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
int g_log_n[256];
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->ref_shift = (int)p->n_del - (int)p->n_ins;
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].ref_shift = (int)q->n_del - (int)q->n_ins;
s->multi[z++].mm = q->n_mm;
}
rest -= q->l - q->k + 1;
} else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here.
int j, i;
for (j = rest, i = q->l - q->k + 1; 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].ref_shift = (int)q->n_del - (int)q->n_ins;
s->multi[z++].mm = q->n_mm;
}
rest = 0;
break;
}
}
s->n_multi = z;
}
}
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];
}
bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int ref_len, int *strand)
{
bwtint_t pos_f;
int is_rev;
pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base
*strand = !is_rev;
if (is_rev) pos_f = pos_f + 1 < ref_len? 0 : pos_f - ref_len + 1; // position of the first base
return pos_f; // FIXME: it is possible that pos_f < bns->anns[ref_id].offset
}
/**
* 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 bntseq_t *bns, const bwt_t *bwt, bwa_seq_t *seq, const int max_mm, const float fnr)
{
int max_diff, strand;
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;
seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
//fprintf(stderr, "%d\n", seq->ref_shift);
seq->pos = bwa_sa2pos(bns, bwt, seq->sa, seq->len + seq->ref_shift, &strand);
seq->strand = strand;
seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
if (seq->pos == (bwtint_t)-1) seq->type = BWA_TYPE_NO_MATCH;
}
void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
{
int i, j, strand, n_multi;
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) {
bwa_seq_t *p = &seqs[i];
bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
for (j = n_multi = 0; j < p->n_multi; ++j) {
bwt_multi1_t *q = p->multi + j;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + p->ref_shift, &strand);
q->strand = strand;
if (q->pos != p->pos && q->pos != (bwtint_t)-1)
p->multi[n_multi++] = *q;
}
p->n_multi = n_multi;
}
bwt_destroy(bwt);
}
#define SW_BW 50
bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, ubyte_t *seq, int ref_shift, bwtint_t rb, int *n_cigar)
{
bwa_cigar_t *cigar = 0;
uint32_t *cigar32 = 0;
ubyte_t *rseq;
int64_t k, re, rlen;
int8_t mat[25];
bwa_fill_scmat(1, 3, mat);
re = rb + len + ref_shift;
assert(re <= l_pac);
rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
assert(re - rb == rlen);
ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension
cigar = (bwa_cigar_t*)cigar32;
for (k = 0; k < *n_cigar; ++k)
cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
free(rseq);
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_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 && 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;
}
}
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)
{
ubyte_t *pacseq;
int i, j, k;
kstring_t *str;
if (!_pacseq) {
pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
err_rewind(bns->fp_pac);
err_fread_noeof(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 = k = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap) { // gapped alignment
q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, q->ref_shift, q->pos, &n_cigar);
q->n_cigar = n_cigar;
if (q->cigar) s->multi[k++] = *q;
} else s->multi[k++] = *q;
}
s->n_multi = k; // this squeezes out gapped alignments which failed the CIGAR generation
if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, s->ref_shift, s->pos, &s->n_cigar);
if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
}
// 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, pacseq, str, &nm);
s->nm = nm;
}
}
free(str->s); free(str);
// correct for trimmed reads
for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
if (!_pacseq) free(pacseq);
}
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_seq(FILE *stream, bwa_seq_t *seq) {
char buffer[4096];
const int bsz = sizeof(buffer);
int i, j, l;
if (seq->strand == 0) {
for (i = 0; i < seq->full_len; i += bsz) {
l = seq->full_len - i > bsz ? bsz : seq->full_len - i;
for (j = 0; j < l; j++) buffer[j] = "ACGTN"[seq->seq[i + j]];
err_fwrite(buffer, 1, l, stream);
}
} else {
for (i = seq->full_len - 1; i >= 0; i -= bsz) {
l = i + 1 > bsz ? bsz : i + 1;
for (j = 0; j < l; j++) buffer[j] = "TGCAN"[seq->seq[i - j]];
err_fwrite(buffer, 1, l, stream);
}
}
}
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_cnt_ambi(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;
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
bns_cnt_ambi(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
bwa_print_seq(stdout, p);
err_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[0]) 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_cnt_ambi(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);
}
}
}
err_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);
//Why did this work differently to the version above??
//for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
bwa_print_seq(stdout, p);
err_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[0]) 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);
err_putchar('\n');
}
}
void bwase_initialize()
{
int i;
for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
}
void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
{
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;
FILE *fp_sa;
gap_opt_t opt;
char magic[4];
// initialization
bwase_initialize();
bns = bns_restore(prefix);
srand48(bns->seed);
fp_sa = xopen(fn_sa, "r");
m_aln = 0;
err_fread_noeof(magic, 1, 4, fp_sa);
if (strncmp(magic, SAI_MAGIC, 4) != 0) {
fprintf(stderr, "[E::%s] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.\n", __func__);
exit(1);
}
err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa);
bwa_print_sam_hdr(bns, rg_line);
//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;
err_fread_noeof(&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);
}
err_fread_noeof(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(bns, 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);
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);
bns_destroy(bns);
err_fclose(fp_sa);
free(aln);
}
int bwa_sai2sam_se(int argc, char *argv[])
{
int c, n_occ = 3;
char *prefix, *rg_line = 0;
while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
switch (c) {
case 'h': break;
case 'r':
if ((rg_line = bwa_set_rg(optarg)) == 0) 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;
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
return 1;
}
bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
free(prefix);
return 0;
}
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