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r511: fixed wrong primary sam record

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Heng Li
2017-10-12 23:02:18 -04:00
parent dea3b60918
commit 858213d513
3 changed files with 8 additions and 5 deletions
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pe.c
+6 -3
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@@ -117,13 +117,18 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
r[0] = a[max_idx[0]].r, r[1] = a[max_idx[1]].r;
r[0]->proper_frag = r[1]->proper_frag = 1;
for (s = 0; s < 2; ++s) {
if (r[s]->id != r[s]->parent) {
if (r[s]->id != r[s]->parent) { // then lift to primary and update parent
mm_reg1_t *p = &regs[s][r[s]->parent];
for (i = 0; i < n_regs[s]; ++i)
if (regs[s][i].parent == p->id)
regs[s][i].parent = r[s]->id;
p->mapq = 0;
}
if (!r[s]->sam_pri) { // then sync sam_pri
for (i = 0; i < n_regs[s]; ++i)
regs[s][i].sam_pri = 0;
r[s]->sam_pri = 1;
}
}
mapq_pe = r[0]->mapq > r[1]->mapq? r[0]->mapq : r[1]->mapq;
for (i = 0; i < sc.n; ++i)
@@ -144,8 +149,6 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
if (r[1]->mapq < 1) r[1]->mapq = 1;
}
}
mm_set_sam_pri(n_regs[0], regs[0]);
mm_set_sam_pri(n_regs[1], regs[1]);
kfree(km, a);
kfree(km, sc.a);