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r711: assign proper mapq to primary inversions

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Heng Li
2018-02-15 14:34:59 -05:00
parent a0d62519c1
commit 8fc5f8dc90
4 changed files with 32 additions and 5 deletions
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hit.c
+28 -1
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@@ -408,7 +408,33 @@ void mm_seg_free(void *km, int n_segs, mm_seg_t *segs)
kfree(km, segs);
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr)
static void mm_set_inv_mapq(void *km, int n_regs, mm_reg1_t *regs)
{
int i, n_aux;
uint64_t *aux;
if (n_regs < 3) return;
for (i = 0; i < n_regs; ++i)
if (regs[i].inv) break;
if (i == n_regs) return; // no inversion hits
aux = (uint64_t*)kmalloc(km, n_regs * 8);
for (i = n_aux = 0; i < n_regs; ++i)
if (regs[i].parent == i || regs[i].parent < 0)
aux[n_aux++] = (uint64_t)regs[i].as << 32 | i;
radix_sort_64(aux, aux + n_aux);
for (i = 1; i < n_aux - 1; ++i) {
mm_reg1_t *inv = &regs[(int32_t)aux[i]];
if (inv->inv) {
mm_reg1_t *l = &regs[(int32_t)aux[i-1]];
mm_reg1_t *r = &regs[(int32_t)aux[i+1]];
inv->mapq = l->mapq < r->mapq? l->mapq : r->mapq;
}
}
kfree(km, aux);
}
void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr)
{
static const float q_coef = 40.0f;
int64_t sum_sc = 0;
@@ -451,4 +477,5 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
if (r->p && r->p->dp_max > r->p->dp_max2 && r->mapq == 0) r->mapq = 1;
} else r->mapq = 0;
}
mm_set_inv_mapq(km, n_regs, regs);
}