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r122: filter contained aln after DP extension

This commit is contained in:
Heng Li 2017-06-30 15:23:30 -04:00
parent fce87ce7bd
commit 646a746cdc
4 changed files with 39 additions and 3 deletions
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30
hit.c
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@ -79,6 +79,35 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r) // and compu
kfree(km, w);
}
void mm_update_parent(void *km, float mask_level, int n, mm_reg1_t *r) // due to changes to r.{qs,qe} after DP extension
{
int i, j, k, *w, n_pri = 0;
if (n <= 0) return;
for (i = 0; i < n; ++i)
if (r[i].id == r[i].parent) ++n_pri;
if (n_pri <= 1) return;
w = (int*)kmalloc(km, n_pri * sizeof(int));
for (i = j = 0; i < n; ++i) // find the first primary
if (r[i].id == r[i].parent) break;
for (w[0] = i, i = i + 1, k = 1; i < n; ++i) {
int si = r[i].qs, ei = r[i].qe;
if (r[i].id != r[i].parent) continue; // only check primary
for (j = 0; j < k; ++j) {
int sj = r[w[j]].qs, ej = r[w[j]].qe;
int min = ej - sj < ei - si? ej - sj : ei - si;
int ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si);
if (ol > mask_level * min) {
r[i].parent = r[w[j]].parent;
if (r[w[j]].subsc < r[i].score)
r[w[j]].subsc = r[i].score;
break;
}
}
if (j == k) w[k++] = i;
}
kfree(km, w);
}
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id
{
int *tmp, i, max_id = -1, n_tmp, n_pri;
@ -109,7 +138,6 @@ void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_;
mm_set_parent(km, mask_level, n, r);
for (i = k = 0; i < n; ++i)
if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
r[k++] = r[i];

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r121-pre"
#define MM_VERSION "2.0-r122-pre"
void liftrlimit()
{

8
map.c
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@ -238,11 +238,17 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
regs = mm_gen_regs(b->km, qlen, n_u, u, a);
*n_regs = n_u;
if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
mm_join_long(b->km, opt, qlen, *n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}
if (opt->flag & MM_F_CIGAR)
if (opt->flag & MM_F_CIGAR) {
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
if (!(opt->flag & MM_F_AVA)) {
mm_update_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
}
}
mm_set_mapq(*n_regs, regs);
// free

2
mmpriv.h
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@ -39,6 +39,8 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a);
void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r);
void mm_update_parent(void *km, float mask_level, int n, mm_reg1_t *r);
void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r);
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a);
void mm_set_mapq(int n_regs, mm_reg1_t *regs);