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r461: randomize repetitive hits

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Heng Li
2017-10-04 13:05:18 -04:00
parent cf55c84056
commit 2a1e738a94
6 changed files with 52 additions and 25 deletions
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12
pe.c
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@@ -94,15 +94,15 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
q = a[last[a[i].rev]].r;
if (r->rid != q->rid || r->rs - q->re > max_gap_ref) continue;
for (j = last[a[i].rev]; j >= 0; --j) {
int64_t sum;
int64_t score;
if (a[j].rev != a[i].rev || a[j].s == a[i].s) continue;
q = a[j].r;
if (r->rid != q->rid || r->rs - q->re > max_gap_ref) break;
if (r->p->dp_max + q->p->dp_max < dp_thres) continue;
sum = r->p->dp_max + q->p->dp_max;
if (sum > max)
max = sum, max_idx[a[j].s] = j, max_idx[a[i].s] = i;
kv_push(uint64_t, km, sc, sum);
score = (int64_t)(r->p->dp_max + q->p->dp_max) | (r->hash + q->hash);
if (score > max)
max = score, max_idx[a[j].s] = j, max_idx[a[i].s] = i;
kv_push(uint64_t, km, sc, score);
}
} else { // forward first read or reverse second read
last[a[i].rev] = i;
@@ -138,7 +138,7 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
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]) {
} else if (max>>32 > sc.a[sc.n - 2]>>32) {
if (r[0]->mapq < 1) r[0]->mapq = 1;
if (r[1]->mapq < 1) r[1]->mapq = 1;
}