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r211: a better heurstic to reduce false seeds

This commit is contained in:
Heng Li 2017-07-26 23:56:38 -04:00
parent 8b08a2ec41
commit 371e20cc7c
2 changed files with 19 additions and 22 deletions
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39
align.c
View File

@ -158,24 +158,6 @@ static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2],
}
}
static void mm_filter_bad_seeds(int n, mm128_t *a, int max_space, int max_diff)
{
int i;
if (n < 3) return;
for (i = 0; i < n - 2; ++i) {
int32_t q[3], t[3], gap01, gap12, gap02;
t[0] = (int32_t)a[i].x, q[0] = (int32_t)a[i].y;
t[1] = (int32_t)a[i+1].x, q[1] = (int32_t)a[i+1].y;
t[2] = (int32_t)a[i+2].x, q[2] = (int32_t)a[i+2].y;
if (t[2] - t[0] > max_space || q[2] - q[0] > max_space) continue;
gap01 = (t[1] - t[0]) - (q[1] - q[0]), gap01 = gap01 > 0? gap01 : -gap01;
gap12 = (t[2] - t[1]) - (q[2] - q[1]), gap12 = gap12 > 0? gap12 : -gap12;
gap02 = (t[2] - t[0]) - (q[2] - q[0]), gap02 = gap02 > 0? gap02 : -gap02;
if (gap01 + gap12 - gap02 > max_diff)
a[++i].y |= 1ULL << 41;
}
}
static void mm_skip_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int32_t *as, int32_t *cnt)
{
int32_t i, l;
@ -223,7 +205,6 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_skip_ends(r, a, opt->bw, &as1, &cnt1);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
mm_filter_bad_seeds(cnt1, &a[as1], opt->max_gap, 100);
// compute rs0 and qs0
if (r->split && as1 > 0) {
@ -270,10 +251,26 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < cnt1; ++i) { // gap filling
if (a[as1+i].y>>41&1) continue;
int gap, to_patch = 0;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
gap = (qe - qs) - (re - rs);
if (gap < -40 || gap > 40) {
int g, j, i_next = -1;
for (j = i + 1; j < cnt1; ++j) {
if ((int32_t)a[as1 + j].y - qs > opt->max_gap || (int32_t)a[as1 + j].x - rs > opt->max_gap) break;
g = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
if (abs(gap + g) < 0.5f * abs(gap - g)) {
i_next = j;
break;
}
}
if (i_next > i) {
i = i_next, to_patch = 1;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
}
}
re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
if (i == cnt1 - 1 || to_patch || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
int bw1 = bw;
if (a[as1+i].y>>40&1)
bw1 = qe - qs > re - rs? qe - qs : re - rs;

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r206-dirty"
#define MM_VERSION "2.0-r211-dirty"
void liftrlimit()
{