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better seeding

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chhylp123
2021-08-22 09:53:34 -04:00
parent bfff640a82
commit 37b07e4d33
15 changed files with 637 additions and 406 deletions
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rcut.cpp
+6 -6
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@@ -889,9 +889,9 @@ trans_chain* t_ch)
offset += (uint32_t)u->a[i];
if(i >= sid && i <= eid)
{
if(t_ch->is_r_het[u->a[i]>>33] != t->hs)
if(t_ch->ir_het[u->a[i]>>33] != t->hs)
{
fprintf(stderr, "ERROR-d: is_r_het: %u, h_status: %u\n", t_ch->is_r_het[u->a[i]>>33], t->hs);
fprintf(stderr, "ERROR-d: is_r_het: %u, h_status: %u\n", t_ch->ir_het[u->a[i]>>33], t->hs);
}
}
}
@@ -939,11 +939,11 @@ void update_mc_edges(mc_g_t *mg, hap_overlaps_list* ha, kv_u_trans_t *ta, trans_
u = &(mg->ug->u.a[v]);
for (k = 1, l = 0, offset = 0, l_pos = 0; k <= u->n; ++k)
{
if (k == u->n || t_ch->is_r_het[u->a[k]>>33] != t_ch->is_r_het[u->a[l]>>33])
if (k == u->n || t_ch->ir_het[u->a[k]>>33] != t_ch->ir_het[u->a[l]>>33])
{
kv_pushp(mc_interval_t, p, &t);
t->uID = v;
t->hs = t_ch->is_r_het[u->a[l]>>33];
t->hs = t_ch->ir_het[u->a[l]>>33];
t->bS = l_pos;
t->bE = offset + mg->rg->seq[u->a[k-1]>>33].len - 1;
@@ -2680,10 +2680,10 @@ void set_p_flag(mc_g_t *mg, uint32_t uID, uint8_t* trio_flag, trans_chain* t_ch,
for (i = 0; i < u->n; i++)
{
trio_flag[u->a[i]>>33] |= SET_TRIO;
if(t_ch->is_r_het[u->a[i]>>33] == N_HET) continue;
if(t_ch->ir_het[u->a[i]>>33] == N_HET) continue;
if(s == 0)
{
if(t_ch->is_r_het[u->a[i]>>33]&P_HET)//special case
if(t_ch->ir_het[u->a[i]>>33]&P_HET)//special case
{
trio_flag[u->a[i]>>33] |= FATHER;
}