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update 0.15.5

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chhylp123
2021-07-22 00:59:52 -04:00
parent a531a4cbda
commit 62b7418257
16 changed files with 1146 additions and 68 deletions
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Overlaps.cpp
+30 -19
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@@ -13220,6 +13220,8 @@ long long gap_fuzz, bub_label_t* b_mask_t)
{
hic_clean(sg);
ug_opt_t opt; memset(&opt, 0, sizeof(opt));
kvec_pe_hit *rhits = NULL;
ma_ug_t *ug_fa = NULL, *ug_mo = NULL;
opt.coverage_cut = coverage_cut;
opt.sources = sources;
opt.reverse_sources = reverse_sources;
@@ -13289,18 +13291,18 @@ 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, &opt, 0);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch, &opt, 0, asm_opt.scffold?&rhits:NULL);
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
if(!rhits && cov) destory_hap_cov_t(&cov);
if(!rhits && t_ch) destory_trans_chain(&t_ch);
char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
sprintf(gfa_name, "%s.after.clean_d_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
free(gfa_name);
// char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
// sprintf(gfa_name, "%s.after.clean_d_utg.noseq.gfa", output_file_name);
// FILE* output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
// free(gfa_name);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
@@ -13329,10 +13331,18 @@ long long gap_fuzz, bub_label_t* b_mask_t)
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
ug_fa = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t);
ug_mo = output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t);
if(rhits)
{
ha_aware_order(rhits, sg, ug_fa, ug_mo, cov?&(cov->t_ch->k_trans):&(t_ch->k_trans), &opt, 3);
kv_destroy(rhits->a); kv_destroy(rhits->idx); kv_destroy(rhits->occ); free(rhits);
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
ma_ug_destroy(ug_fa); ma_ug_destroy(ug_mo);
}
}
ma_ug_t *get_poly_ug(asg_t *sg, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
@@ -13416,7 +13426,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(t_ch, output_file_name);
}
hic_analysis(ug, sg, t_ch, &opt, 0);
hic_analysis(ug, sg, t_ch, &opt, 0, NULL);
destory_trans_chain(&t_ch);
ma_ug_destroy(ug);
asg_cleanup(sg);
@@ -17102,7 +17112,6 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
fprintf(stderr, "Writing %s to disk... \n", gfa_name);
FILE* output_file = NULL;
if(is_bench == 0) output_file = fopen(gfa_name, "w");
@@ -17128,16 +17137,18 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
///debug_utg_graph(ug, sg, 0, 0);
///debug_untig_length(ug, tipsLen, gfa_name);
///print_untig_by_read(ug, "m64011_190901_095311/125831121/ccs", 2310925, "end");
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
if(is_bench)
{
free(gfa_name);
kv_destroy(new_rtg_edges.a);
return ug;
}
fprintf(stderr, "Writing %s to disk... \n", gfa_name);
///debug_utg_graph(ug, sg, 0, 0);
///debug_untig_length(ug, tipsLen, gfa_name);
///print_untig_by_read(ug, "m64011_190901_095311/125831121/ccs", 2310925, "end");
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, (flag==FATHER?"h1tg":"h2tg"), output_file);
fclose(output_file);