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This commit is contained in:
Heng Li 2017-06-24 22:51:31 -04:00
parent d08b58d21f
commit aa5881e7bb
4 changed files with 43 additions and 13 deletions
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26
align.c
View File

@ -1,6 +1,7 @@
#include <assert.h>
#include <string.h>
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
#ifndef kroundup32
@ -29,6 +30,21 @@ static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
t = seq[i], seq[i] = seq[len - 1 - i], seq[len - 1 - i] = t;
}
static void mm_reg_split(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
{
if (n <= 0 || n >= r->cnt) return;
*r2 = *r;
r2->p = 0;
r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
r2->as = r->as + n;
mm_reg_set_coor(r2, qlen, a);
r->cnt -= r2->cnt;
r->score -= r2->score;
mm_reg_set_coor(r, qlen, a);
r->split = r2->split = 1;
}
static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, uint32_t n_cigar, uint32_t *cigar)
{
uint32_t k, l, toff = 0, qoff = 0;
@ -119,6 +135,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
bw = (int)(opt->bw * 1.5 + 1.);
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);
@ -171,8 +188,15 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
int j;
for (j = i - 1; j >= 0; --j)
if ((int32_t)a[r->as + j].x < re + ez->max_t)
break;
r->p->score += ez->max;
abort();
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
mm_reg_split(r, r2, j + 1, qlen, a);
break;
} else {
r->p->score += ez->score;
}

12
map.c
View File

@ -168,18 +168,8 @@ mm_reg1_t *mm_gen_reg(int qlen, int n_u, uint64_t *u, mm128_t *a)
ri->parent = -1, ri->subsc = 0;
ri->score = u[i]>>32;
ri->cnt = (int32_t)u[i];
ri->rev = a[k].x>>63;
ri->rid = a[k].x<<1>>33;
ri->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
ri->re = (int32_t)a[k + ri->cnt - 1].x + 1;
if (!ri->rev) {
ri->qs = (int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32);
ri->qe = (int32_t)a[k + ri->cnt - 1].y + 1;
} else {
ri->qs = qlen - ((int32_t)a[k + ri->cnt - 1].y + 1);
ri->qe = qlen - ((int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32));
}
ri->as = k;
mm_reg_set_coor(ri, qlen, a);
k += ri->cnt;
}
return r;

2
minimap.h
View File

@ -51,7 +51,7 @@ typedef struct {
} mm_extra_t;
typedef struct {
uint32_t cnt:31, rev:1;
uint32_t cnt:30, rev:1, split:1;
uint32_t rid:31, rep:1;
int32_t score;
int32_t qs, qe, rs, re;

16
mmpriv.h
View File

@ -22,4 +22,20 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
#endif
static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
{
int32_t k = r->as;
r->rev = a[k].x>>63;
r->rid = a[k].x<<1>>33;
r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
r->re = (int32_t)a[k + r->cnt - 1].x + 1;
if (!r->rev) {
r->qs = (int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32);
r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
} else {
r->qs = qlen - ((int32_t)a[k + r->cnt - 1].y + 1);
r->qe = qlen - ((int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32));
}
}
#endif