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#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#include "bntseq.h"
#include "bwt_lite.h"
#include "utils.h"
#include "bwtsw2.h"
#include "stdaln.h"
#include "kstring.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
#include "ksort.h"
#define __left_lt(a, b) ((a).end > (b).end)
KSORT_INIT(hit, bsw2hit_t, __left_lt)
extern unsigned char nst_nt4_table[256];
unsigned char nt_comp_table[256] = {
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n',
'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
};
extern int bsw2_resolve_duphits(const bwt_t *bwt, bwtsw2_t *b, int IS);
extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level);
bsw2opt_t *bsw2_init_opt()
{
bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
o->bw = 50;
o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0;
o->mask_level = 0.50f; o->yita = 5.5f; o->coef = 5.5f;
o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
return o;
}
void bsw2_destroy(bwtsw2_t *b)
{
int i;
if (b == 0) return;
if (b->cigar)
for (i = 0; i < b->n; ++i) free(b->cigar[i]);
free(b->cigar); free(b->n_cigar); free(b->hits);
free(b);
}
#define __gen_ap(par, opt) do { \
int i; \
for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b; \
for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \
(par).gap_open = (opt)->q; (par).gap_ext = (opt)->r; \
(par).gap_end = (opt)->r; \
(par).row = 5; (par).band_width = opt->bw; \
} while (0)
#define __rpac(pac, l, i) (pac[(l-i-1)>>2] >> (~(l-i-1)&3)*2 & 0x3)
void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem)
{
int i, matrix[25];
bwtint_t k;
uint8_t *target = 0, *query;
AlnParam par;
par.matrix = matrix;
__gen_ap(par, opt);
query = calloc(lq, 1);
// sort according to the descending order of query end
ks_introsort(hit, b->n, b->hits);
target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
// reverse _query
for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
// core loop
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
int score, j;
path_t path;
p->n_seeds = 1;
if (p->l || p->k == 0) continue;
for (j = score = 0; j < i; ++j) {
bsw2hit_t *q = b->hits + j;
if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
if (q->n_seeds < (1<<14) - 2) ++q->n_seeds;
++score;
}
}
if (score) continue;
if (lt > p->k) lt = p->k;
if (is_rev) {
for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
target[j++] = __rpac(pac, l_pac, k);
} else {
for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
}
lt = j;
score = aln_extend_core(target, lt, query + lq - p->beg, p->beg, &par, &path, 0, p->G, _mem);
if (score > p->G) { // extensible
p->G = score;
p->len += path.i;
p->beg -= path.j;
p->k -= path.i;
}
}
free(query); free(target);
}
void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem)
{
int i, matrix[25];
uint32_t k;
uint8_t *target;
AlnParam par;
par.matrix = matrix;
__gen_ap(par, opt);
target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
int j, score;
path_t path;
if (p->l) continue;
if (is_rev) {
for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
target[j++] = __rpac(pac, l_pac, k);
} else {
for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
}
lt = j;
score = aln_extend_core(target, lt, query + p->beg, lq - p->beg, &par, &path, 0, 1, _mem);
// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
if (score >= p->G) {
p->G = score;
p->len = path.i;
p->end = path.j + p->beg;
}
}
free(target);
}
/* generate CIGAR array(s) in b->cigar[] */
static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], uint8_t *pac, bwtsw2_t *b)
{
uint8_t *target;
int i, matrix[25];
AlnParam par;
path_t *path;
par.matrix = matrix;
__gen_ap(par, opt);
i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
target = calloc(i, 1);
path = calloc(i + lq, sizeof(path_t));
// memory clean up for b
if (b->n < b->max) {
b->max = b->n;
b->hits = realloc(b->hits, b->n * sizeof(bsw2hit_t));
}
if (b->cigar) free(b->cigar);
if (b->n_cigar) free(b->n_cigar);
b->cigar = (uint32_t**)calloc(b->max, sizeof(void*));
b->n_cigar = (int*)calloc(b->max, sizeof(int));
// generate CIGAR
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
uint8_t *query;
uint32_t k;
int score, path_len, beg, end;
if (p->l) continue;
beg = (p->flag & 0x10)? lq - p->end : p->beg;
end = (p->flag & 0x10)? lq - p->beg : p->end;
query = seq[(p->flag & 0x10)? 1 : 0] + beg;
for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
b->cigar[i] = aln_path2cigar32(path, path_len, &b->n_cigar[i]);
if (beg != 0 || end < lq) { // write soft clipping
b->cigar[i] = realloc(b->cigar[i], 4 * (b->n_cigar[i] + 2));
if (beg != 0) {
memmove(b->cigar[i] + 1, b->cigar[i], b->n_cigar[i] * 4);
b->cigar[i][0] = beg<<4 | 4;
++b->n_cigar[i];
}
if (end < lq) {
b->cigar[i][b->n_cigar[i]] = (lq - end)<<4 | 4;
++b->n_cigar[i];
}
}
}
free(target); free(path);
}
/* this is for the debugging purpose only */
void bsw2_debug_hits(const bwtsw2_t *b)
{
int i;
printf("# raw hits: %d\n", b->n);
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
if (p->l == 0)
printf("%d, %d, %d, %u, %u\n", p->G, p->beg, p->end, p->k, p->l);
}
}
static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse)
{
int i;
if (b[0]->n + b[1]->n > b[0]->max) {
b[0]->max = b[0]->n + b[1]->n;
b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t));
}
for (i = 0; i < b[1]->n; ++i) {
bsw2hit_t *p = b[0]->hits + b[0]->n + i;
*p = b[1]->hits[i];
if (is_reverse) {
int x = p->beg;
p->beg = l - p->end;
p->end = l - x;
p->flag |= 0x10;
}
}
b[0]->n += b[1]->n;
bsw2_destroy(b[1]);
b[1] = 0;
}
/* seq[0] is the forward sequence and seq[1] is the reverse complement. */
static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target,
int l, uint8_t *seq[2], int is_rev, bsw2global_t *pool)
{
extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]);
bwtsw2_t *b[2], **bb[2];
int k;
for (k = 0; k < 2; ++k) {
bwtl_t *query = bwtl_seq2bwtl(l, seq[k]);
bb[k] = bsw2_core(opt, query, target, pool);
bwtl_destroy(query);
}
b[0] = bb[0][1]; b[1] = bb[1][1]; // bb[*][1] are "narrow SA hits"
bsw2_chain_filter(opt, l, b);
for (k = 0; k < 2; ++k) {
bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem);
merge_hits(bb[k], l, 0); // bb[k][1] is merged to bb[k][0] here
bsw2_resolve_duphits(0, bb[k][0], 0);
bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem);
b[k] = bb[k][0];
free(bb[k]);
}
merge_hits(b, l, 1); // again, b[1] is merged to b[0]
bsw2_resolve_query_overlaps(b[0], opt->mask_level);
return b[0];
}
/* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */
static void flag_fr(bwtsw2_t *b[2])
{
int i, j;
for (i = 0; i < b[0]->n; ++i) {
bsw2hit_t *p = b[0]->hits + i;
p->flag |= 0x10000;
}
for (i = 0; i < b[1]->n; ++i) {
bsw2hit_t *p = b[1]->hits + i;
p->flag |= 0x20000;
}
for (i = 0; i < b[0]->n; ++i) {
bsw2hit_t *p = b[0]->hits + i;
for (j = 0; j < b[1]->n; ++j) {
bsw2hit_t *q = b[1]->hits + j;
if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
q->flag |= 0x30000; p->flag |= 0x30000;
break;
}
}
}
}
typedef struct {
int l, tid;
char *name, *seq, *qual, *sam;
} bsw2seq1_t;
typedef struct {
int n, max;
bsw2seq1_t *seq;
} bsw2seq_t;
static int fix_cigar(const char *qname, const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
{
// FIXME: this routine does not work if the query bridge three reference sequences
int32_t coor, refl, lq;
int x, y, i, seqid;
bns_coor_pac2real(bns, p->k, p->len, &seqid);
coor = p->k - bns->anns[seqid].offset;
refl = bns->anns[seqid].len;
x = coor; y = 0;
// test if the alignment goes beyond the boundary
for (i = 0; i < n_cigar; ++i) {
int op = cigar[i]&0xf, ln = cigar[i]>>4;
if (op == 1 || op == 4 || op == 5) y += ln;
else if (op == 2) x += ln;
else x += ln, y += ln;
}
lq = y; // length of the query sequence
if (x > refl) { // then fix it
int j, nc, mq[2], nlen[2];
uint32_t *cn, kk = 0;
nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0;
cn = calloc(n_cigar + 3, 4);
x = coor; y = 0;
for (i = j = 0; i < n_cigar; ++i) {
int op = cigar[i]&0xf, ln = cigar[i]>>4;
if (op == 4 || op == 5 || op == 1) { // ins or clipping
y += ln;
cn[j++] = cigar[i];
} else if (op == 2) { // del
if (x + ln >= refl && nc == 0) {
cn[j++] = (uint32_t)(lq - y)<<4 | 4;
nc = j;
cn[j++] = (uint32_t)y<<4 | 4;
kk = p->k + (x + ln - refl);
nlen[0] = x - coor;
nlen[1] = p->len - nlen[0] - ln;
} else cn[j++] = cigar[i];
x += ln;
} else if (op == 0) { // match
if (x + ln >= refl && nc == 0) {
// FIXME: not consider a special case where a split right between M and I
cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M
cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S
nc = j;
mq[0] += refl - x;
cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4;
if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0;
mq[1] += x + ln - refl;
kk = bns->anns[seqid].offset + refl;
nlen[0] = refl - coor;
nlen[1] = p->len - nlen[0];
} else {
cn[j++] = cigar[i];
mq[nc?1:0] += ln;
}
x += ln; y += ln;
}
}
if (mq[0] > mq[1]) { // then take the first alignment
n_cigar = nc;
memcpy(cigar, cn, 4 * nc);
p->len = nlen[0];
} else {
p->k = kk; p->len = nlen[1];
n_cigar = j - nc;
memcpy(cigar, cn + nc, 4 * (j - nc));
}
free(cn);
}
return n_cigar;
}
/* generate SAM lines for a sequence in ks with alignment stored in
* b. ks->name and ks->seq will be freed and set to NULL in the end. */
static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b)
{
int i, k;
kstring_t str;
memset(&str, 0, sizeof(kstring_t));
if (b == 0 || b->n == 0) { // no hits
ksprintf(&str, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t", ks->name);
for (i = 0; i < ks->l; ++i) kputc(ks->seq[i], &str);
if (ks->qual) {
kputc('\t', &str);
for (i = 0; i < ks->l; ++i) kputc(ks->qual[i], &str);
} else kputs("\t*", &str);
kputc('\n', &str);
}
for (i = 0; b && i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
int32_t seqid = -1, coor = -1;
int j, qual, nn = 0;
int beg, end;
if (p->l == 0) {
b->n_cigar[i] = fix_cigar(ks->name, bns, p, b->n_cigar[i], b->cigar[i]);
nn = bns_coor_pac2real(bns, p->k, p->len, &seqid);
coor = p->k - bns->anns[seqid].offset;
}
ksprintf(&str, "%s\t%d", ks->name, p->flag&0x10);
ksprintf(&str, "\t%s\t%d", seqid>=0? bns->anns[seqid].name : "*", coor + 1);
if (p->l == 0) {
{ // estimate mapping quality
float c = 1.0;
int subo = p->G2 > opt->t? p->G2 : opt->t;
if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
if (p->n_seeds < 2) c *= .2;
qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499);
if (qual > 250) qual = 250;
if (p->flag&1) qual = 0;
}
ksprintf(&str, "\t%d\t", qual);
for (k = 0; k < b->n_cigar[i]; ++k)
ksprintf(&str, "%d%c", b->cigar[i][k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[b->cigar[i][k]&0xf]);
} else ksprintf(&str, "\t0\t*");
ksprintf(&str, "\t*\t0\t0\t");
beg = 0; end = ks->l;
if (opt->hard_clip) {
if ((b->cigar[i][0]&0xf) == 4) beg += b->cigar[i][0]>>4;
if ((b->cigar[i][b->n_cigar[i]-1]&0xf) == 4) end -= b->cigar[i][b->n_cigar[i]-1]>>4;
}
for (j = beg; j < end; ++j) {
if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str);
else kputc(ks->seq[j], &str);
}
if (ks->qual) {
kputc('\t', &str);
for (j = beg; j < end; ++j) {
if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str);
else kputc(ks->qual[j], &str);
}
} else ksprintf(&str, "\t*");
ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tXN:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, nn);
if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
kputc('\n', &str);
}
ks->sam = str.s;
free(ks->seq); ks->seq = 0;
free(ks->qual); ks->qual = 0;
free(ks->name); ks->name = 0;
}
/* Core routine to align reads in _seq. It is separated from
* process_seqs() to realize multi-threading */
static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2])
{
int x;
bsw2opt_t opt = *_opt;
bsw2global_t *pool = bsw2_global_init();
for (x = 0; x < _seq->n; ++x) {
bsw2seq1_t *p = _seq->seq + x;
uint8_t *seq[2], *rseq[2];
int i, l, k;
bwtsw2_t *b[2];
l = p->l;
#ifdef HAVE_PTHREAD
if (x % _opt->n_threads != tid) continue;
#endif
// set opt->t
opt.t = _opt->t;
if (opt.t < log(l) * opt.coef) opt.t = (int)(log(l) * opt.coef + .499);
if (pool->max_l < l) { // then enlarge working space for aln_extend_core()
int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l;
pool->max_l = l;
pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24);
}
// set opt->bw
opt.bw = _opt->bw;
k = (l * opt.a - 2 * opt.q) / (2 * opt.r + opt.a);
i = (l * opt.a - opt.a - opt.t) / opt.r;
if (k > i) k = i;
if (k < 1) k = 1; // I do not know if k==0 causes troubles
opt.bw = _opt->bw < k? _opt->bw : k;
// set seq[2] and rseq[2]
seq[0] = calloc(l * 4, 1);
seq[1] = seq[0] + l;
rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l;
// convert sequences to 2-bit representation
for (i = k = 0; i < l; ++i) {
int c = nst_nt4_table[(int)p->seq[i]];
if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled
seq[0][i] = c;
seq[1][l-1-i] = 3 - c;
rseq[0][l-1-i] = c;
rseq[1][i] = 3 - c;
}
if (l - k < opt.t) { // too few unambiguous bases
print_hits(bns, &opt, p, 0);
free(seq[0]); continue;
}
// alignment
b[0] = bsw2_aln1_core(&opt, bns, pac, target[0], l, seq, 0, pool);
for (k = 0; k < b[0]->n; ++k)
if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
if (k < b[0]->n) {
b[1] = bsw2_aln1_core(&opt, bns, pac, target[1], l, rseq, 1, pool);
for (i = 0; i < b[1]->n; ++i) {
bsw2hit_t *p = b[1]->hits + i;
int x = p->beg;
p->beg = l - p->end;
p->end = l - x;
if (p->l == 0) p->k = bns->l_pac - (p->k + p->len);
}
flag_fr(b);
merge_hits(b, l, 0);
bsw2_resolve_duphits(0, b[0], 0);
bsw2_resolve_query_overlaps(b[0], opt.mask_level);
} else b[1] = 0;
// generate CIGAR and print SAM
gen_cigar(&opt, l, seq, pac, b[0]);
print_hits(bns, &opt, p, b[0]);
// free
free(seq[0]);
bsw2_destroy(b[0]);
}
bsw2_global_destroy(pool);
}
#ifdef HAVE_PTHREAD
typedef struct {
int tid;
bsw2seq_t *_seq;
const bsw2opt_t *_opt;
const bntseq_t *bns;
uint8_t *pac;
bwt_t *target[2];
} thread_aux_t;
/* another interface to bsw2_aln_core() to facilitate pthread_create() */
static void *worker(void *data)
{
thread_aux_t *p = (thread_aux_t*)data;
bsw2_aln_core(p->tid, p->_seq, p->_opt, p->bns, p->pac, p->target);
return 0;
}
#endif
/* process sequences stored in _seq, generate SAM lines for these
* sequences and reset _seq afterwards. */
static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2])
{
int i;
#ifdef HAVE_PTHREAD
if (opt->n_threads <= 1) {
bsw2_aln_core(0, _seq, opt, bns, pac, target);
} else {
pthread_t *tid;
pthread_attr_t attr;
thread_aux_t *data;
int j;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
for (j = 0; j < opt->n_threads; ++j) {
thread_aux_t *p = data + j;
p->tid = j; p->_seq = _seq; p->_opt = opt; p->bns = bns;
p->pac = pac; p->target[0] = target[0]; p->target[1] = target[1];
pthread_create(&tid[j], &attr, worker, p);
}
for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
free(data); free(tid);
}
#else
bsw2_aln_core(0, _seq, opt, bns, pac, target);
#endif
// print and reset
for (i = 0; i < _seq->n; ++i) {
bsw2seq1_t *p = _seq->seq + i;
if (p->sam) printf("%s", p->sam);
free(p->name); free(p->seq); free(p->qual); free(p->sam);
p->tid = -1; p->l = 0;
p->name = p->seq = p->qual = p->sam = 0;
}
fflush(stdout);
_seq->n = 0;
}
void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn)
{
gzFile fp;
kseq_t *ks;
int l, size = 0;
uint8_t *pac;
bsw2seq_t *_seq;
pac = calloc(bns->l_pac/4+1, 1);
if (pac == 0) {
fprintf(stderr, "[bsw2_aln] insufficient memory!\n");
return;
}
for (l = 0; l < bns->n_seqs; ++l)
printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
fp = xzopen(fn, "r");
ks = kseq_init(fp);
_seq = calloc(1, sizeof(bsw2seq_t));
while ((l = kseq_read(ks)) >= 0) {
bsw2seq1_t *p;
if (_seq->n == _seq->max) {
_seq->max = _seq->max? _seq->max<<1 : 1024;
_seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
}
p = &_seq->seq[_seq->n++];
p->tid = -1;
p->l = l;
p->name = strdup(ks->name.s);
p->seq = strdup(ks->seq.s);
p->qual = ks->qual.l? strdup(ks->qual.s) : 0;
p->sam = 0;
size += l;
if (size > opt->chunk_size) {
fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size);
process_seqs(_seq, opt, bns, pac, target);
size = 0;
}
}
fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size);
process_seqs(_seq, opt, bns, pac, target);
free(_seq->seq); free(_seq);
kseq_destroy(ks);
gzclose(fp);
free(pac);
}