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r450: differentiate exact repeats via mapq

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Heng Li
2017-09-27 23:51:05 -04:00
parent a13691d00d
commit 935a6e6064
3 changed files with 9 additions and 1 deletions
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pe.c
+7
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@@ -135,6 +135,13 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
}
if (r[0]->mapq < mapq_pe) r[0]->mapq = (r[0]->mapq + mapq_pe) / 2;
if (r[1]->mapq < mapq_pe) r[1]->mapq = (r[1]->mapq + mapq_pe) / 2;
if (sc.n == 1) {
if (r[0]->mapq < 2) r[0]->mapq = 2;
if (r[1]->mapq < 2) r[1]->mapq = 2;
} else if (max > sc.a[sc.n - 2]) {
if (r[0]->mapq < 1) r[0]->mapq = 1;
if (r[1]->mapq < 1) r[1]->mapq = 1;
}
}
kfree(km, a);