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update unitig distance

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chhylp123
2021-04-12 04:54:06 -04:00
parent 7235f6426f
commit 36afbce9bc
7 changed files with 1038 additions and 44 deletions
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hic.cpp
+3 -13
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@@ -3441,7 +3441,7 @@ static void worker_for_dis(void *data, long i, int tid)
if(t->e.a[k].del) continue;
u = t->e.a[k].uID;
for (v = ((uint64_t)(i)<<1); v < ((uint64_t)(i+1)<<1); v++)
for (v = ((uint64_t)(i)<<1); v < ((uint64_t)(i+1)<<1); v++)///two directions
{
d[0] = d[1] = db[0] = db[1] = (uint64_t)-1;
for (j = 0; j < M->matrix.a[v].a.n; j++)
@@ -3462,9 +3462,9 @@ static void worker_for_dis(void *data, long i, int tid)
t->e.a[k].dis = min<<1;
t->e.a[k].dis += min_b;
t->e.a[k].dis <<=1;
t->e.a[k].dis += v&1;
t->e.a[k].dis += v&1;//s-direction
t->e.a[k].dis <<=1;
t->e.a[k].dis += min_i;
t->e.a[k].dis += min_i;//e-direction
}
}
@@ -13397,28 +13397,18 @@ 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++)
{
///fprintf(stderr, "0********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_r_het);
///fprintf(stderr, "1********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
if(bub.round_id == 0)
{
///fprintf(stderr, "2********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_links(sl.idx, &sl.hits, &link, &bub, &M);
///fprintf(stderr, "3********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_reverse_links(&link, idx->ug, &bub);
///fprintf(stderr, "4********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
}
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, &link, &bub, &back_hc_edge, &M, &hap, 0);
///fprintf(stderr, "5********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///init_hic_p_new((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
///fprintf(stderr, "6********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
init_contig_partition(&hap, idx, &bub, &link);
///fprintf(stderr, "7********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
phasing_improvement(&hap, &(hap.g_p), idx, &bub, &link);
///fprintf(stderr, "8********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
label_unitigs(&(hap.g_p), idx->ug);
///fprintf(stderr, "9********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///print_hc_links(idx->link, 0, &hap);
}