xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-02 10:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

add "n-weight"

Browse Source
This commit is contained in:
chhylp123
2021-04-24 00:03:36 -04:00
parent 7b07e355b7
commit c972c64b39
5 changed files with 71 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hic.cpp
+18 -8
View File
@@ -2284,10 +2284,6 @@ uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label)
hom_occ++;
}
}
// if(uid == 18759)
// {
// fprintf(stderr, "het_occ: %u, hom_occ: %u\n", het_occ, hom_occ);
// }
if((het_occ+hom_occ) == 0) return n_het_label; ///hom
if((het_occ > ((het_occ+hom_occ)*0.8)) && ((het_occ+hom_occ) > m_het_occ)) return m_het_label; ///must het
@@ -9271,7 +9267,7 @@ H_partition* hap, int8_t *s, trans_idx* dis)
dis->med = ((buf.n&1)?buf.a[buf.n>>1]:((buf.a[buf.n>>1]+buf.a[(buf.n>>1)-1])/2));
}
fprintf(stderr, "dis->med: %lu\n", dis->med);
// fprintf(stderr, "dis->med: %lu\n", dis->med);
kv_destroy(buf);
return 1;
@@ -13017,8 +13013,8 @@ void update_trans_g(ha_ug_index* idx, kv_u_trans_t *ta, bubble_type* bub)
// append_boundary_chain_hic(idx->ug, ta, bub);
fprintf(stderr, "s_bub: %lu, f_bub: %lu, b_bub: %lu, b_end_bub: %lu, tangle_bub: %lu, cross_bub: %lu, mess_bub: %lu\n",
bub->s_bub, bub->f_bub, bub->b_bub, bub->b_end_bub, bub->tangle_bub, bub->cross_bub, bub->mess_bub);
// fprintf(stderr, "s_bub: %lu, f_bub: %lu, b_bub: %lu, b_end_bub: %lu, tangle_bub: %lu, cross_bub: %lu, mess_bub: %lu\n",
// bub->s_bub, bub->f_bub, bub->b_bub, bub->b_end_bub, bub->tangle_bub, bub->cross_bub, bub->mess_bub);
///reorder_bubbles(bub, ta, idx->ug->g->n_seq);
// fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
@@ -14206,6 +14202,18 @@ void destory_ps_t(ps_t **s)
free((*s));
}
void verbose_het_stat(bubble_type *bub)
{
uint64_t i, hetBase = 0, homBase = 0;
for (i = 0; i < bub->ug->g->n_seq; i++)
{
if(IF_HOM(i, *bub)) homBase += bub->ug->g->seq[i].len;
else hetBase += bub->ug->g->seq[i].len;
}
fprintf(stderr, "[M::stat] # heterozygous bases: %lu; # homozygous bases: %lu\n", hetBase, homBase);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
@@ -14241,7 +14249,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
mb_nodes_t u;
kv_init(u.bid); kv_init(u.idx); kv_init(u.u);
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = 2;
bub.round_id = 0; bub.n_round = asm_opt.n_weight;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
@@ -14267,6 +14275,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
**/
}
verbose_het_stat(&bub);
///print_hc_links(&link, 0, &hap);
// print_kv_u_trans(&k_trans, &link, s->s);