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low hamming for sampels with low het rate

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chhylp123
2021-06-09 20:10:50 -04:00
parent ca67e7a9b3
commit 9dc530cbfb
3 changed files with 105 additions and 20 deletions
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hic.cpp
+17 -16
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@@ -6173,7 +6173,8 @@ inline double get_trans_weight_advance(const ha_ug_index* idx, uint64_t x, trans
}
else
{
rate = 0.2;
// rate = 0.2;
rate = 0.4;
}
@@ -13633,11 +13634,11 @@ void resolve_bubble_chain_by_hic(ha_ug_index *idx, kv_u_trans_t *ta, bubble_type
// }
// }
for (i = 0; i < edges.a.n; i++)
{
fprintf(stderr, "s-utg%.6lul<------>d-utg%.6ul\n", (edges.a.a[i].ul>>33) + 1, (edges.a.a[i].v>>1) + 1);
// for (i = 0; i < edges.a.n; i++)
// {
// fprintf(stderr, "s-utg%.6lul<------>d-utg%.6ul\n", (edges.a.a[i].ul>>33) + 1, (edges.a.a[i].v>>1) + 1);
}
// }
/*******************************for debug************************************/
if(edges.a.n > 0)
{
@@ -15250,11 +15251,11 @@ void print_kv_weight(kv_u_trans_t *ta)
fprintf(stderr, "*********ta->n: %u\n", (uint32_t)ta->n);
for (i = 0; i < ta->n; i++)
{
fprintf(stderr, "+qn(%u)->tn(%u): %f\n", ta->a[i].qn, ta->a[i].tn, ta->a[i].nw);
fprintf(stderr, "+s-utg%.6ul->d-utg%.6ul: %f\n", ta->a[i].qn+1, ta->a[i].tn+1, ta->a[i].nw);
get_u_trans_spec(ta, ta->a[i].tn, ta->a[i].qn, &e, NULL);
if(e)
{
fprintf(stderr, "-tn(%u)->qn(%u): %f\n", e->qn, e->tn, e->nw);
fprintf(stderr, "-d-utg%.6ul->s-utg%.6ul: %f\n", e->qn+1, e->tn+1, e->nw);
}
else
{
@@ -15693,12 +15694,12 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
{
bub.round_id = bub.n_round;
label_unitigs_sm(s->s, NULL, idx->ug);
goto skip_flipping;
}
// if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
// {
// bub.round_id = bub.n_round;
// label_unitigs_sm(s->s, NULL, idx->ug);
// goto skip_flipping;
// }
s = init_ps_t(11, idx->ug->g->n_seq);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
@@ -15726,9 +15727,9 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
label_unitigs(&(hap.g_p), idx->ug);
**/
}
write_ps_t(s, asm_opt.output_file_name);
// write_ps_t(s, asm_opt.output_file_name);
skip_flipping:
// skip_flipping:
verbose_het_stat(&bub);
// print_kv_weight(&k_trans);
@@ -15886,7 +15887,7 @@ int hic_short_align_poy(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx,
// }
/*******************************for debug************************************/
}
// write_psg_t(s, asm_opt.output_file_name);
write_psg_t(s, asm_opt.output_file_name);
skip_flipping:
verbose_het_stat(&bub);