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r373

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chhylp123
2021-09-10 17:17:44 -04:00
parent 17b5cb21d3
commit 809ca18dda
18 changed files with 1569 additions and 1031 deletions
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50
rcut.cpp
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@@ -2767,6 +2767,48 @@ void clean_ovlp_by_mc(mc_g_t *mg, hap_overlaps_list* ha)
}
void filter_ta_by_mc(ma_ug_t *ug, asg_t *read_g, uint32_t uID, kv_u_trans_t* ta, mc_match_t *ma, int8_t *s)
{
mc_edge_t *o = pt_a(*ma, uID);
uint32_t n = pt_n(*ma, uID), k, qn, tn;
u_trans_t *p = NULL;
for (k = 0; k < n; ++k)
{
qn = ma_x(o[k]); tn = ma_y(o[k]); p = NULL;
if((s[qn]*s[tn])!=-1) continue;
get_u_trans_spec(ta, qn, tn, &p, NULL);
if(p && p->nw == o[k].w) {
p->del = 0;
}
else {
get_u_trans_spec(ta, tn, qn, &p, NULL);
if(p && p->nw == o[k].w) p->del = 0;
}
if(!p) fprintf(stderr, "ERROR-ta-p\n");
}
}
void clean_ta_by_mc(mc_g_t *mg, kv_u_trans_t *ta)
{
uint32_t v, i;
u_trans_t *p = NULL;
for (i = 0; i < ta->n; i++) ta->a[i].del = 1;
for (i = 0; i < mg->e->n_seq; ++i) filter_ta_by_mc(mg->ug, mg->rg, i, ta, mg->e, mg->s.a);
for (i = v = 0; i < ta->n; i++) {
if(ta->a[i].del) continue;
ta->a[v++] = ta->a[i];
}
ta->n = v;
for (i = 0; i < v; i++) {
kv_pushp(u_trans_t, *ta, &p);
(*p) = ta->a[i];
p->qn = ta->a[i].tn; p->qs = ta->a[i].ts; p->qe = ta->a[i].te;
p->tn = ta->a[i].qn; p->ts = ta->a[i].qs; p->te = ta->a[i].qe;
}
kt_u_trans_t_idx(ta, mg->ug->g->n_seq);
}
void p_nodes(mc_g_t *mg, trans_chain* t_ch, uint8_t* trio_flag)
{
uint32_t i;
@@ -2844,7 +2886,7 @@ void print_hap_s(int8_t *s, uint32_t sn)
}
}
void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag, uint32_t renew_s, int8_t *s, uint32_t is_sys, bubble_type* bub, kv_u_trans_t *ref)
void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag, uint32_t renew_s, int8_t *s, uint32_t is_sys, bubble_type* bub, kv_u_trans_t *ref, int clean_ov)
{
mc_opt_t opt;
mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
@@ -2863,8 +2905,10 @@ void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_u
p_nodes(mg, t_ch, trio_flag);
}
if(ovlp) clean_ovlp_by_mc(mg, ovlp);
if(clean_ov){
if(ovlp) clean_ovlp_by_mc(mg, ovlp);
if(ta) clean_ta_by_mc(mg, ta);
}
// print_hap_s(s, ug->u.n);
destory_mc_g_t(&mg);