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fixed duplicated chaining issue

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chhylp123
2022-05-03 17:35:43 -04:00
parent 8138941a26
commit e8399b18f1
7 changed files with 270 additions and 112 deletions
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9
gfa_ut.cpp
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@@ -1328,6 +1328,8 @@ void fill_containment_by_ul(asg_t *g, ma_hit_t_alloc *src)
}
void ul_clean_gfa(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
double ou_drop_rate, int64_t max_tip, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, char *o_file)
{
@@ -1345,6 +1347,8 @@ double ou_drop_rate, int64_t max_tip, bub_label_t *b_mask_t, int32_t is_ou, int3
// debug_info_of_specfic_node("m64011_190830_220126/95028102/ccs", sg, rI, "beg");
asg_arc_cut_tips(sg, max_tip, &bu, is_ou);
// fprintf(stderr, "[M::%s] count_edges_v_w(sg, 49778, 49847)->%ld\n", __func__, count_edges_v_w(sg, 49778, 49847));
for (i = 0; i < clean_round; i++, drop += step) {
if(drop > max_ovlp_drop_ratio) drop = max_ovlp_drop_ratio;
// fprintf(stderr, "(0):i->%ld, drop->%f\n", i, drop);
@@ -1406,7 +1410,6 @@ double ou_drop_rate, int64_t max_tip, bub_label_t *b_mask_t, int32_t is_ou, int3
// mini_overlap_length, bubble_dist, 10);
set_hom_global_coverage(&asm_opt, sg, uopt->coverage_cut, src, rev, rI, uopt->max_hang, uopt->min_ovlp);
rescue_bubble_by_chain(sg, uopt->coverage_cut, src, rev, (asm_opt.max_short_tip*2), 0.15, 3, rI, 0.05, 0.9, uopt->max_hang, uopt->min_ovlp, 10, uopt->gap_fuzz, b_mask_t);
output_unitig_graph(sg, uopt->coverage_cut, o_file, src, rI, uopt->max_hang, uopt->min_ovlp);
// flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
flat_soma_v(sg, src, rI);
@@ -1418,6 +1421,10 @@ double ou_drop_rate, int64_t max_tip, bub_label_t *b_mask_t, int32_t is_ou, int3
}
if(is_ou) {
for (i = 0; i < (int64_t)sg->n_seq; ++i) {
if(sg->seq[i].del) continue;
sg->seq[i].c = PRIMARY_LABLE;
}
hic_clean(sg);
ul_realignment(uopt, sg);
// if(ul_refine_alignment(uopt, sg)) update_sg_uo(sg, src);