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r524: reverted to bwa-mem end bonus

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and reduced the cost of clipping when filtering by identity
This commit is contained in:
Heng Li
2017-10-20 16:57:31 -04:00
parent 15ed0712c2
commit bd04372873
4 changed files with 9 additions and 5 deletions
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hit.c
+2 -2
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@@ -286,7 +286,7 @@ void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden
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? 0.5f : 0.025f * (qual[j] - 33);
n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
blen += r->qs - en;
}
assert(r->p);
@@ -295,7 +295,7 @@ void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden
en = en > r->qe? en : r->qe;
}
for (j = en; j < qlen; ++j)
n_diff += qual == 0 || qual[j] >= 53? 0.5f : 0.025f * (qual[j] - 33);
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)