zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r213: more careful solution to wrong seeds 

a little better, but not good enough!
This commit is contained in:
Heng Li 2017-07-27 13:19:11 -04:00
parent b927838495
commit 2c79580649
2 changed files with 53 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

76
align.c
View File

@ -158,7 +158,54 @@ static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2],
}
}
static void mm_skip_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int32_t *as, int32_t *cnt)
static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min_gap, int diff_thres, int max_ext_len, int max_ext_cnt)
{
int max_st, max_en, n, i, k, max;
int *K;
for (i = 1, n = 0; i < cnt1; ++i) { // count the number of gaps longer than min_gap
int gap = ((int32_t)a[as1 + i].y - a[as1 + i - 1].y) - ((int32_t)a[as1 + i].x - a[as1 + i - 1].x);
if (gap < -min_gap || gap > min_gap) ++n;
}
if (n <= 1) return;
K = (int*)kmalloc(km, n * sizeof(int));
for (i = 1, n = 0; i < cnt1; ++i) { // store the positions of long gaps
int gap = ((int32_t)a[as1 + i].y - a[as1 + i - 1].y) - ((int32_t)a[as1 + i].x - a[as1 + i - 1].x);
if (gap < -min_gap || gap > min_gap)
K[n++] = i;
}
max = 0, max_st = max_en = -1;
for (k = 0;; ++k) { // traverse long gaps
int gap, l, n_ins = 0, n_del = 0, qs, rs, max_diff = 0, max_diff_l = -1;
if (k == n || k >= max_en) {
if (max_en > 0)
for (i = K[max_st]; i < K[max_en]; ++i)
a[as1 + i].y |= 1ULL << 41;
max = 0, max_st = max_en = -1;
if (k == n) break;
}
i = K[k];
gap = ((int32_t)a[as1 + i].y - a[as1 + i - 1].y) - ((int32_t)a[as1 + i].x - a[as1 + i - 1].x);
if (gap > 0) n_ins += gap;
else n_del += -gap;
qs = (int32_t)a[as1 + i - 1].y;
rs = (int32_t)a[as1 + i - 1].x;
for (l = k + 1; l < n && l <= k + max_ext_cnt; ++l) {
int j = K[l], diff;
if ((int32_t)a[as1 + j].y - qs > max_ext_len || (int32_t)a[as1 + j].x - rs > max_ext_len) break;
gap = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
if (gap > 0) n_ins += gap;
else n_del += -gap;
diff = n_ins + n_del - abs(n_ins - n_del);
if (max_diff < diff)
max_diff = diff, max_diff_l = l;
}
if (max_diff > diff_thres && max_diff > max)
max = max_diff, max_st = k, max_en = max_diff_l;
}
kfree(km, K);
}
static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int32_t *as, int32_t *cnt)
{
int32_t i, l;
*as = r->as, *cnt = r->cnt;
@ -202,7 +249,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
bw = (int)(opt->bw * 1.5 + 1.);
r2->cnt = 0;
mm_skip_ends(r, a, opt->bw, &as1, &cnt1);
mm_fix_bad_ends(r, a, opt->bw, &as1, &cnt1);
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
@ -251,30 +299,10 @@ 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
int gap, to_patch = 0;
if (a[as1+i].y>>41&1) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
gap = ((int32_t)a[as1 + i].y - (int32_t)a[as1 + i - 1].y) - (a[as1 + i].x - a[as1 + i - 1].x);
if (gap < -20 || gap > 20) {
int i_next = -1, j, n_ins = 0, n_del = 0, diff, max_diff = 0;
if (gap < 0) n_del += -gap;
else n_ins += gap;
for (j = i + 1; j < cnt1 && j - i < 20; ++j) {
if ((int32_t)a[as1 + j].y - qs > opt->max_gap>>1 || (int32_t)a[as1 + j].x - rs > opt->max_gap>>1) break;
gap = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
if (gap < 0) n_del += -gap;
else n_ins += gap;
diff = n_ins + n_del - abs(n_ins - n_del);
if (diff >= 40) {
if (diff >= max_diff) max_diff = diff, i_next = j;
} else if (i_next > i) 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 || to_patch || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
if (i == cnt1 - 1 || (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-r212-dirty"
#define MM_VERSION "2.0-r213-dirty"
void liftrlimit()
{