108 lines
2.5 KiB
C
108 lines
2.5 KiB
C
|
#include <stdio.h>
|
||
|
|
#include "bwtsw2.h"
|
||
|
|
|
||
|
|
typedef struct {
|
||
|
|
uint32_t tbeg, tend;
|
||
|
|
int qbeg, qend;
|
||
|
|
uint32_t flag:1, idx:31;
|
||
|
|
int chain; // also reuse as a counter
|
||
|
|
} hsaip_t;
|
||
|
|
|
||
|
|
#define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)
|
||
|
|
|
||
|
|
#include "ksort.h"
|
||
|
|
KSORT_INIT(hsaip, hsaip_t, _hsaip_lt)
|
||
|
|
|
||
|
|
static int chaining(const bsw2opt_t *opt, int shift, int n, hsaip_t *z, hsaip_t *chain)
|
||
|
|
{
|
||
|
|
int j, k, m = 0;
|
||
|
|
ks_introsort(hsaip, n, z);
|
||
|
|
for (j = 0; j < n; ++j) {
|
||
|
|
hsaip_t *p = z + j;
|
||
|
|
for (k = m - 1; k >= 0; --k) {
|
||
|
|
hsaip_t *q = chain + k;
|
||
|
|
int x = p->qbeg - q->qbeg; // always positive
|
||
|
|
int y = p->tbeg - q->tbeg;
|
||
|
|
if (y > 0 && x - y <= opt->bw && y - x <= opt->bw) {
|
||
|
|
if (p->qend > q->qend) q->qend = p->qend;
|
||
|
|
if (p->tend > q->tend) q->tend = p->tend;
|
||
|
|
++q->chain;
|
||
|
|
p->chain = shift + k;
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if (k < 0) {
|
||
|
|
chain[m] = *p;
|
||
|
|
chain[m].chain = 1;
|
||
|
|
chain[m].idx = p->chain = shift + m;
|
||
|
|
++m;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
return m;
|
||
|
|
}
|
||
|
|
|
||
|
|
void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2])
|
||
|
|
{
|
||
|
|
hsaip_t *z[2], *chain[2];
|
||
|
|
int i, j, k, n[2], m[2];
|
||
|
|
char *flag;
|
||
|
|
// initialization
|
||
|
|
n[0] = b[0]->n; n[1] = b[1]->n;
|
||
|
|
z[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
|
||
|
|
z[1] = z[0] + n[0];
|
||
|
|
chain[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
|
||
|
|
for (k = j = 0; k < 2; ++k) {
|
||
|
|
for (i = 0; i < b[k]->n; ++i) {
|
||
|
|
bsw2hit_t *p = b[k]->hits + i;
|
||
|
|
hsaip_t *q = z[k] + i;
|
||
|
|
q->flag = k; q->idx = i;
|
||
|
|
q->tbeg = p->k; q->tend = p->k + p->len;
|
||
|
|
q->chain = -1;
|
||
|
|
q->qbeg = p->beg; q->qend = p->end;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
// chaining
|
||
|
|
m[0] = chaining(opt, 0, n[0], z[0], chain[0]);
|
||
|
|
chain[1] = chain[0] + m[0];
|
||
|
|
m[1] = chaining(opt, m[0], n[1], z[1], chain[1]);
|
||
|
|
// change query coordinate on the reverse strand
|
||
|
|
for (k = 0; k < m[1]; ++k) {
|
||
|
|
hsaip_t *p = chain[1] + k;
|
||
|
|
int tmp = p->qbeg;
|
||
|
|
p->qbeg = len - p->qend; p->qend = len - tmp;
|
||
|
|
}
|
||
|
|
// filtering
|
||
|
|
flag = calloc(m[0] + m[1], 1);
|
||
|
|
ks_introsort(hsaip, m[0] + m[1], chain[0]);
|
||
|
|
for (k = 1; k < m[0] + m[1]; ++k) {
|
||
|
|
hsaip_t *p = chain[0] + k;
|
||
|
|
for (j = 0; j < k; ++j) {
|
||
|
|
hsaip_t *q = chain[0] + j;
|
||
|
|
if (flag[q->idx]) continue;
|
||
|
|
if (q->qend >= p->qend && q->chain > p->chain * opt->t_seeds * 2) {
|
||
|
|
flag[p->idx] = 1;
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
for (k = 0; k < n[0] + n[1]; ++k) {
|
||
|
|
hsaip_t *p = z[0] + k;
|
||
|
|
if (flag[p->chain])
|
||
|
|
b[p->flag]->hits[p->idx].G = 0;
|
||
|
|
}
|
||
|
|
free(flag);
|
||
|
|
// squeeze out filtered elements in b[2]
|
||
|
|
for (k = 0; k < 2; ++k) {
|
||
|
|
for (j = i = 0; j < n[k]; ++j) {
|
||
|
|
bsw2hit_t *p = b[k]->hits + j;
|
||
|
|
if (p->G) {
|
||
|
|
if (i != j) b[k]->hits[i++] = *p;
|
||
|
|
else ++i;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
b[k]->n = i;
|
||
|
|
}
|
||
|
|
// free
|
||
|
|
free(z[0]); free(chain[0]);
|
||
|
|
}
|