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unfinished chain filter

This commit is contained in:
Heng Li 2013-02-04 17:23:06 -05:00
parent c589b42fb5
commit 9d0cdb2d3c
3 changed files with 62 additions and 17 deletions
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74
bwamem.c
View File

@ -6,6 +6,7 @@
#include "kvec.h"
#include "bntseq.h"
#include "ksw.h"
#include "ksort.h"
void mem_fill_scmat(int a, int b, int8_t mat[25])
{
@ -109,6 +110,10 @@ const bwtintv_v *smem_next(smem_i *itr, int split_len)
return itr->matches;
}
/********************************
* Chaining while finding SMEMs *
********************************/
#include "kbtree.h"
#define chain_cmp(a, b) ((a).pos - (b).pos)
@ -196,6 +201,49 @@ mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uin
* Filtering chains *
********************/
typedef struct {
int beg, end, w;
void *p, *p2;
} flt_aux_t;
#define flt_lt(a, b) ((a).w > (b).w)
KSORT_INIT(mem_flt, flt_aux_t, flt_lt)
void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn)
{
flt_aux_t *a;
int i, j, n;
if (chn->n <= 1) return; // no need to filter
a = malloc(sizeof(flt_aux_t) * chn->n);
for (i = 0; i < chn->n; ++i) {
mem_chain1_t *c = &chn->chains[i];
int w = 0;
for (j = 0; j < c->n; ++j) w += c->len;
a[i].beg = c->seeds[0].qbeg;
a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
a[i].w = w;
a[i].p = c;
a[i].w2 = 0; a[i].p2 = 0;
}
ks_introsort(mem_flt, chn->n, a);
for (i = 1, n = 1; i < chn->n; ++i) {
for (j = 0; j < n; ++j) {
int b_max = a[j].beg > a[i].beg? a[j].beg : a[i].beg;
int e_min = e[j].end < a[i].end? a[j].end : a[i].end;
if (e_min > b_max) { // have overlap
int min_l = a[i].end - a[i].beg < a[j].end - a[j].beg? a[i].end - a[i].beg : a[j].end - a[j].beg;
if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
if (a[j].p2 == 0) a[j].p2 = a[i].p;
if (a[i].w < a[j].w * opt->chain_drop_ratio)
break;
}
}
}
if (j == n) a[n++] = a[i]; // if have no significant overlap with better chains, keep it.
}
free(a);
}
/****************************************
* Construct the alignment from a chain *
****************************************/
@ -206,15 +254,14 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
return l > 1? l : 1;
}
mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a)
{ // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds
mem_aln_t a;
int i, j, qbeg;
int64_t rlen, rbeg, rmax[2], tmp;
const mem_seed_t *s;
uint8_t *rseq = 0;
memset(&a, 0, sizeof(mem_aln_t));
memset(a, 0, sizeof(mem_aln_t));
// get the start and end of the seeded region
rbeg = c->seeds[0].rbeg; qbeg = c->seeds[0].qbeg;
// get the max possible span
@ -238,18 +285,16 @@ mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
tmp = rbeg - rmax[0];
rs = malloc(tmp);
for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
a.score = ksw_extend(qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, c->seeds[0].len * opt->a, 0, &qle, &tle);
a.qb = qbeg - qle; a.rb = rbeg - tle;
a->score = ksw_extend(qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, c->seeds[0].len * opt->a, 0, &qle, &tle);
a->qb = qbeg - qle; a->rb = rbeg - tle;
free(qs); free(rs);
} else a.score = c->seeds[0].len * opt->a, a.qb = 0, a.rb = rbeg;
} else a->score = c->seeds[0].len * opt->a, a->qb = 0, a->rb = rbeg;
s = &c->seeds[0];
if (s->qbeg + s->len != l_query) { // right extension of the first seed
int qle, tle, qe, re;
int16_t *qw = 0;
qe = s->qbeg + s->len; re = s->rbeg + s->len - rmax[0];
// for (j = 0; j < l_query - qe; ++j) putchar("ACGTN"[(int)query[j+qe]]); putchar('\n');
// for (j = 0; j < rmax[1] - rmax[0] - re; ++j) putchar("ACGTN"[(int)rseq[j+re]]); putchar('\n');
if (c->n > 1) { // generate $qw
int l = rmax[1] - (s->rbeg + s->len);
qw = malloc(l * 2);
@ -264,19 +309,18 @@ mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
}
}
}
a.score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a.score, qw, &qle, &tle);
a.qe = qe + qle; a.re = rmax[0] + re + tle;
a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, qw, &qle, &tle);
a->qe = qe + qle; a->re = rmax[0] + re + tle;
free(qw);
} else a.qe = l_query, a.re = s->rbeg + s->len;
} else a->qe = l_query, a->re = s->rbeg + s->len;
a.is_all = 1;
a->is_all = 1;
if (c->n > 1) { // check if all the seeds have been included
s = &c->seeds[c->n - 1];
if (s->qbeg + s->len > a.qe) a.is_all = 0;
if (s->qbeg + s->len > a->qe) a->is_all = 0;
}
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\n", c->n, a.score, a.qb, a.qe, a.rb, a.re, a.is_all);
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\n", c->n, a->score, a->qb, a->qe, a->rb, a->re, a->is_all);
free(rseq);
return a;
}

2
bwamem.h
View File

@ -47,7 +47,7 @@ mem_opt_t *mem_opt_init(void);
void mem_fill_scmat(int a, int b, int8_t mat[25]);
mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c);
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a);
#ifdef __cplusplus
}

3
fastmap.c
View File

@ -53,7 +53,8 @@ int main_mem(int argc, char *argv[])
chain = mem_chain(opt, bwt, seq->seq.l, (uint8_t*)seq->seq.s);
for (i = 0; i < chain.n; ++i) {
mem_chain1_t *p = &chain.chains[i];
mem_chain2aln(opt, bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p);
mem_aln_t a;
mem_chain2aln(opt, bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p, &a);
printf("%d\t%d", i, p->n);
for (j = 0; j < p->n; ++j) {
bwtint_t pos;