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collect contig alignment + renew_utg bug fixed

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chhylp123
2021-05-09 17:47:50 -04:00
parent 03adce6202
commit 7918396d21
7 changed files with 431 additions and 19 deletions
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Overlaps.cpp
+19 -1
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@@ -12720,6 +12720,21 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
long long gap_fuzz, bub_label_t* b_mask_t)
{
hic_clean(sg);
ug_opt_t opt; memset(&opt, 0, sizeof(opt));
opt.coverage_cut = coverage_cut;
opt.sources = sources;
opt.reverse_sources = reverse_sources;
opt.tipsLen = (asm_opt.max_short_tip*2);
opt.tip_drop_ratio = 0.15;
opt.stops_threshold = 3;
opt.ruIndex = ruIndex;
opt.chimeric_rate = 0.05;
opt.drop_ratio = 0.9;
opt.max_hang = max_hang;
opt.min_ovlp = min_ovlp;
opt.is_bench = 0;
opt.b_mask_t = b_mask_t;
kvec_asg_arc_t_warp new_rtg_edges, d_edges;
kv_init(new_rtg_edges.a); kv_init(d_edges.a);
@@ -12773,7 +12788,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
fclose(output_file);
free(gfa_name);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch, &opt);
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
@@ -13907,6 +13922,7 @@ void renew_utg(ma_ug_t **ug, asg_t* read_g, kvec_asg_arc_t_warp* edge)
u = &(high_level_ug->u.a[i]);
if(u->m == 0) continue;
merge_unitig_content(u, (*ug), read_g, edge);
high_level_ug->g->seq[i].len = u->len;
}
ma_ug_destroy((*ug));
(*ug) = high_level_ug;
@@ -16115,6 +16131,8 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
set_drop_trio_flag(*ug);
destory_hap_cov_t(&cov);
renew_utg(ug, read_g, new_rtg_edges);
}