fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-25 10:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r545: removed option -i, not working well

Browse Source
This commit is contained in:
Heng Li
2017-10-31 22:23:27 -04:00
parent b8e758df0f
commit cd24dc8834
6 changed files with 3 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hit.c
-39
View File
@@ -264,45 +264,6 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
*n_regs = k;
}
void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden, int qlen, const char *qual) // TODO: make sure it is not beyond the ends of contigs
{
int i, j, n_aux = 0, en, blen = 0;
uint64_t *aux;
float n_diff = 0.0f;
if (n_regs <= 0) return;
for (i = 0; i < n_regs; ++i)
if (regs[i].id == regs[i].parent && regs[i].pe_thru) // sequenced through the fragment; don't filter
return;
for (i = 0; i < n_regs; ++i)
if (regs[i].id == regs[i].parent)
++n_aux;
assert(n_aux >= 1);
aux = (uint64_t*)kmalloc(km, n_aux * 8);
for (i = 0, n_aux = 0; i < n_regs; ++i)
if (regs[i].id == regs[i].parent)
aux[n_aux++] = (uint64_t)regs[i].qs<<32 | i;
radix_sort_64(aux, aux + n_aux);
for (i = 0, en = 0; i < n_aux; ++i) {
mm_reg1_t *r = &regs[(int32_t)aux[i]];
if (r->qs > en) {
for (j = en; j < r->qs; ++j)
n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
blen += r->qs - en;
}
assert(r->p);
blen += r->p->blen2;
n_diff += r->p->n_diff2;
en = en > r->qe? en : r->qe;
}
for (j = en; j < qlen; ++j)
n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
blen += qlen - en;
kfree(km, aux);
if (1.0f - n_diff / blen < min_iden)
for (i = 0; i < n_regs; ++i)
regs[i].iden_flt = 1;
}
int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
{ // squeeze out regions in a[] that are not referenced by regs[]
int i, as = 0;