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r317

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chhylp123
2021-03-27 02:46:48 -04:00
parent 24a19d7976
commit 0605aa1961
6 changed files with 371 additions and 209 deletions
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hic.cpp
+31 -40
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@@ -2564,8 +2564,31 @@ void dfs_bubble(asg_t *g, kvec_t_u32_warp* stack, kvec_t_u32_warp* result, uint3
}
}
uint32_t get_unitig_het_arb(ma_utg_t* u, uint8_t *r_het_flag, uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label)
{
uint32_t k, rId;
uint32_t het_occ, hom_occ;
for (k = 0, het_occ = hom_occ = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
if((r_het_flag[rId] & P_HET)) return m_het_label;
if((r_het_flag[rId] & C_HET) || (r_het_flag[rId] & P_HET))
{
het_occ++;
}
else
{
hom_occ++;
}
}
if((het_occ+hom_occ) == 0) return n_het_label; ///hom
if(het_occ > ((het_occ+hom_occ)*0.8)) return m_het_label; ///must het
if(het_occ >= hom_occ) return p_het_label; ///potential het
return n_het_label; ///hom
}
void update_bub_b_s_idx(bubble_type* bub);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag)
{
asg_cleanup(ug->g);
if (!ug->g->is_symm) asg_symm(ug->g);
@@ -2586,16 +2609,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
memset(bub->b_s_idx.a, -1, bub->b_s_idx.n * sizeof(uint64_t));
CALLOC(bub->index, n_vtx);
for (i = 0; i < ug->g->n_seq; i++)
{
if(ug->g->seq[i].c > 0)
{
bub->index[i] = (ug->g->seq[i].c << 2);
ug->g->seq[i].c = 0;
}
}
for (i = 0; i < ug->g->n_seq; i++) ug->g->seq[i].c = 0;
for (v = 0; v < n_vtx; ++v)
{
@@ -2636,7 +2650,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
if((result.a.n + 3) != b.b.n && (result.a.n + 2) != b.b.n) break;
}
}
if(i == b.b.n)
{
@@ -2675,26 +2688,11 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
kv_push(uint32_t, bub->num, bub->list.n);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
bub->f_bub = bub->num.n - 1; ///bub->s_bub = bub->num.n - 1;
for (i = 0; i < ug->g->n_seq; i++)
{
if((bub->index[i]>>2) == 0)
{
bub->index[i] = (uint32_t)-1; ///hom
}
else
{
if((bub->index[i]>>2) == 1)
{
bub->index[i] = P_het(*bub); ///potential het
}
else
{
bub->index[i] = M_het(*bub); ///must het
}
}
}
for (i = 0; i < ug->g->n_seq; i++)
{
bub->index[i] = get_unitig_het_arb(&(ug->u.a[i]), r_het_flag, M_het(*bub), P_het(*bub), (uint32_t)-1);
}
for (i = 0; i < bub->f_bub; i++)
{
@@ -2747,13 +2745,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
for (i = 0; i < ug->g->n_seq; i++)
{
if(bub->index[i] == M_het(*bub)) bub->index[i] = P_het(*bub);
if(bub->index[i] > P_het(*bub))
{
if(het_flag && het_flag[i])
{
bub->index[i] = P_het(*bub);
}
}
}
}
else
@@ -13223,7 +13214,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
bub.round_id = 0; bub.n_round = 2;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_het);
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_r_het);
if(bub.round_id == 0)
{
collect_hc_links(sl.idx, &sl.hits, &link, &bub, &M);