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#include <stdio.h>
#include "bwtsw2.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
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 < opt->max_chain_gap && y < opt->max_chain_gap && x - y <= opt->bw && y - x <= opt->bw) { // chained
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;
} else if (q->chain > opt->t_seeds * 2) k = 0; // if the chain is strong enough, do not check the previous chains
}
if (k < 0) { // not added to any previous chains
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], thres = opt->t_seeds * 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;
}
//for (k = 0; k < m[0]; ++k) printf("%d, [%d,%d), [%d,%d)\n", chain[0][k].chain, chain[0][k].tbeg, chain[0][k].tend, chain[0][k].qbeg, chain[0][k].qend);
// 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 * thres && p->chain < thres) {
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]);
}