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chhylp123
2021-05-24 19:43:50 -04:00
parent 9e6dde7fb2
commit a39f01f4d8
9 changed files with 1696 additions and 567 deletions
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hic.cpp
+53 -11
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@@ -2317,7 +2317,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
if(ug->g->seq[v>>1].del) continue;
if(asg_arc_n(ug->g, v) < 2) continue;
if((bub->index[v]&(uint32_t)3) != 0) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0, NULL))
{
//beg is v, end is b.S.a[0]
//note b.b include end, does not include beg
@@ -2338,7 +2338,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
for (v = 0; v < n_vtx; ++v)
{
if((bub->index[v]&(uint32_t)3) !=2) continue;
if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0, NULL))
{
//note b.b include end, does not include beg
i = b.b.n + 1;
@@ -2370,7 +2370,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
if((bub->num.a[k]>>31) == 0) bub->s_bub++;
v = (bub->num.a[k]<<1)>>1;
bub->num.a[k] = bub->list.n;
if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0, NULL))
{
kv_push(uint64_t, bub->pathLen, pathLen);
//beg is v, end is b.S.a[0]
@@ -2948,7 +2948,7 @@ uint32_t get_specific_shortest_path(pdq_spec *p)
asg_arc_t *av = NULL;
if(p->v == (uint64_t)-1)
{
reset_pdq(p->pq);
// reset_pdq(p->pq);
p->pq->dis.a[p->src] = 0;
if(p->pre) p->pre[p->src] = (uint32_t)-1;
push_pdq(p->pq, p->src, 0);
@@ -2984,17 +2984,40 @@ uint32_t get_specific_shortest_path(pdq_spec *p)
return 0;
}
uint32_t check_trans_relation_by_path(uint32_t v, uint32_t w, pdq* pqv, pdq* pqw,
asg_t *sg, uint8_t *dest, uint8_t df, uint32_t df_occ, uint32_t* pre, double rate)
void get_utg_path(uint64_t s, uint64_t e, uint32_t *path, buf_t *res)
{
uint64_t p = path[e], i;
res->b.n = 0;
kv_push(uint32_t, res->b, e);
while (p != s)
{
kv_push(uint32_t, res->b, p);
p = path[p];
}
kv_push(uint32_t, res->b, s);
for (i = 0; i < (res->b.n>>1); i++)
{
p = res->b.a[i];
res->b.a[i] = res->b.a[res->b.n-i-1];
res->b.a[res->b.n-i-1] = p;
}
res->b.n--;
}
uint32_t check_trans_relation_by_path(uint32_t v, uint32_t w, pdq* pqv, uint32_t* path_v, buf_t *resv,
pdq* pqw, uint32_t* path_w, buf_t *resw, asg_t *sg, uint8_t *dest, uint8_t df, uint32_t df_occ,
double rate, long long *dis)
{
uint64_t r1, r2, d1, d2;
pdq_spec p1, p2, *p = NULL;
p1.v = (uint64_t)-1; p1.src = v; p1.pq = pqv; p1.sg = sg; p1.df_occ = df_occ;
p1.occ = df_occ; p1.flag = df; p1.dest = dest; p1.pre = pre;
p1.occ = df_occ; p1.flag = df; p1.dest = dest; p1.pre = path_v; if(resv) resv->b.n = 0;
reset_pdq(p1.pq);
p2.v = (uint64_t)-1; p2.src = w; p2.pq = pqw; p2.sg = sg; p2.df_occ = df_occ;
p2.occ = df_occ; p2.flag = df; p2.dest = dest; p2.pre = pre;
p2.occ = df_occ; p2.flag = df; p2.dest = dest; p2.pre = path_w; if(resw) resw->b.n = 0;
reset_pdq(p2.pq);
if(dis) (*dis) = 0;
while (1)
{
@@ -3007,11 +3030,22 @@ asg_t *sg, uint8_t *dest, uint8_t df, uint32_t df_occ, uint32_t* pre, double rat
{
if(d2 <= d1*(1+rate) && d2 >= d1*(1-rate))
{
if(resv) get_utg_path(p1.src, p->v, p1.pre, resv);
if(resw) get_utg_path(p2.src, p->v, p2.pre, resw);
if(dis)
{
(*dis) = d1 + d2;
(*dis) -= (sg->seq[p1.src>>1].len + sg->seq[p2.src>>1].len);
}
// fprintf(stderr, "p-utg%.6ul(d1-%lu), a-utg%.6ul(d2-%lu), conver-utg%.6lul\n",
// (v>>1) + 1, d1, (w>>1) + 1, d2, (p->v>>1) + 1);
return 1;
}
}
}
p = &p2;
r2 = get_specific_shortest_path(p);
if(r2 && p1.pq->vis.a[p->v] && p2.pq->vis.a[p->v])
@@ -3021,11 +3055,19 @@ asg_t *sg, uint8_t *dest, uint8_t df, uint32_t df_occ, uint32_t* pre, double rat
{
if(d2 <= d1*(1+rate) && d2 >= d1*(1-rate))
{
if(resv) get_utg_path(p1.src, p->v, p1.pre, resv);
if(resw) get_utg_path(p2.src, p->v, p2.pre, resw);
if(dis)
{
(*dis) = d1 + d2;
(*dis) -= (sg->seq[p1.src>>1].len + sg->seq[p2.src>>1].len);
}
// fprintf(stderr, "p-utg%.6ul(d1-%lu), a-utg%.6ul(d2-%lu), conver-utg%.6lul\n",
// (v>>1) + 1, d1, (w>>1) + 1, d2, (p->v>>1) + 1);
return 1;
}
}
}
if(!r1 && !r2) return 0;
}