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r161: filter bad seeds; changed default -g/-r

This commit is contained in:
Heng Li 2017-07-08 13:31:27 -04:00
parent 1fee5f8edc
commit 38b2830e18
4 changed files with 24 additions and 4 deletions
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20
align.c
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@ -158,6 +158,24 @@ 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_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
{
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
@ -174,6 +192,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
r2->cnt = 0;
mm_adjust_minier(mi, qseq0, &a[r->as], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[r->as + r->cnt - 1], &re, &qe);
mm_filter_bad_seeds(r->cnt, &a[r->as], opt->max_gap, 100);
// compute rs0 and qs0
if (r->split && r->as > 0) {
@ -220,6 +239,7 @@ 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 < r->cnt; ++i) { // gap filling
if (a[r->as+i].y>>41&1) continue;
mm_adjust_minier(mi, qseq0, &a[r->as + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == r->cnt - 1 || (a[r->as+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {

2
hit.c
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@ -183,7 +183,7 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
if (r->cnt < opt->min_cnt) flt = 1;
else {
int blen = r->qe - r->qs < r->re - r->rs? r->qe - r->qs : r->re - r->rs;
if (r->score < blen * opt->min_seedcov_ratio) flt = 1;
if (r->score < blen * opt->min_seedcov_ratio * opt->a) flt = 1;
}
if (r->p) {
if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r160-pre"
#define MM_VERSION "2.0-r161-pre"
void liftrlimit()
{

4
map.c
View File

@ -17,8 +17,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->min_cnt = 3;
opt->min_chain_score = 40;
opt->bw = 1000;
opt->max_gap = 10000;
opt->bw = 500;
opt->max_gap = 5000;
opt->max_chain_skip = 15;
opt->min_seedcov_ratio = 0.0f;