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r153: sam primary record not set sometimes

This commit is contained in:
Heng Li 2017-07-03 13:18:57 -04:00
parent a94bc31311
commit e07daad7ad
4 changed files with 17 additions and 6 deletions
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19
hit.c
View File

@ -126,9 +126,20 @@ void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r)
kfree(km, t);
}
int mm_set_sam_pri(int n, mm_reg1_t *r)
{
int i, n_pri = 0;
for (i = 0; i < n; ++i)
if (r[i].id == r[i].parent) {
++n_pri;
r[i].sam_pri = (n_pri == 1);
} else r[i].sam_pri = 0;
return n_pri;
}
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;
int *tmp, i, max_id = -1, n_tmp;
if (n_regs <= 0) return;
for (i = 0; i < n_regs; ++i) // NB: doesn't work if mm_reg1_t::id is negative
max_id = max_id > regs[i].id? max_id : regs[i].id;
@ -137,7 +148,7 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
for (i = 0; i < n_tmp; ++i) tmp[i] = -1;
for (i = 0; i < n_regs; ++i)
if (regs[i].id >= 0) tmp[regs[i].id] = i;
for (i = n_pri = 0; i < n_regs; ++i) {
for (i = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i];
r->id = i;
if (r->parent == MM_PARENT_TMP_PRI)
@ -145,11 +156,9 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
else if (r->parent >= 0 && tmp[r->parent] >= 0)
r->parent = tmp[r->parent];
else r->parent = MM_PARENT_UNSET;
if (r->id == r->parent) {
if (n_pri++ == 0) r->sam_pri = 1;
}
}
kfree(km, tmp);
mm_set_sam_pri(n_regs, regs);
}
void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r)

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r151-pre"
#define MM_VERSION "2.0-r153-pre"
void liftrlimit()
{

1
map.c
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@ -249,6 +249,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
if (!(opt->flag & MM_F_AVA)) {
mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
mm_set_sam_pri(*n_regs, regs);
}
}
mm_set_mapq(*n_regs, regs);

1
mmpriv.h
View File

@ -42,6 +42,7 @@ 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);
int mm_set_sam_pri(int n, mm_reg1_t *r);
void mm_set_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 best_n, int *n_, mm_reg1_t *r);
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);