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update unitig distance

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chhylp123
2021-04-12 04:54:06 -04:00
parent 7235f6426f
commit 36afbce9bc
7 changed files with 1038 additions and 44 deletions
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Overlaps.cpp
+60 -27
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@@ -9261,7 +9261,8 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
{
fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\tHG:A:%c\n", name, l, "+-"[p->a[j]>>32&1],
(int)Get_NAME_LENGTH((*RNF), x), Get_NAME((*RNF), x),
coverage_cut[x].s, coverage_cut[x].e, x, "apmaaa"[RNF->trio_flag[x]]);
coverage_cut[x].s, coverage_cut[x].e, x,
"apmaaa"[((RNF->trio_flag[x]!=FATHER && RNF->trio_flag[x]!=MOTHER)?AMBIGU:RNF->trio_flag[x])]);
}
else
{
@@ -12355,6 +12356,54 @@ void destory_hc_links(hc_links* link)
kv_destroy(link->enzymes);
}
void print_utg(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_arc_t_warp* new_rtg_edges)
{
if(asm_opt.b_low_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
&asm_opt.b_low_cov, NULL, asm_opt.m_rate);
}
if(asm_opt.b_high_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0);
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.p_ctg.gfa", output_file_name);
fprintf(stderr, "Writing %s to disk... \n", gfa_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
fclose(output_file);
sprintf(gfa_name, "%s.p_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
fclose(output_file);
if(asm_opt.bed_inconsist_rate != 0)
{
sprintf(gfa_name, "%s.p_ctg.lowQ.bed", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges,
max_hang, min_ovlp, asm_opt.bed_inconsist_rate, "ptg", output_file, NULL);
fclose(output_file);
}
free(gfa_name);
/*******************************for debug************************************/
// uint32_t i;
// for (i = 0; i < sg->n_seq; i++)
// {
// if(R_INF.trio_flag[i] == FATHER || R_INF.trio_flag[i] == MOTHER) fprintf(stderr, "ERROR\n");
// }
/*******************************for debug************************************/
}
void hic_clean(asg_t* read_g)
{
uint32_t n_vtx, v, u;
@@ -12479,6 +12528,10 @@ bub_label_t* b_mask_t)
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
@@ -13166,15 +13219,13 @@ void filter_u_trans_t(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, uint32_t thr
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g)
{
kt_u_trans_t_idx(ta, ug->g->n_seq);
kt_u_trans_t_symm(ta, ug);
fprintf(stderr, "+cov->t_ch->k_trans.n: %u\n", (uint32_t)ta->n);
filter_u_trans_t(ta, ug, read_g, 3);
fprintf(stderr, "-cov->t_ch->k_trans.n: %u\n", (uint32_t)ta->n);
debug_u_trans_t(ta);
}
void output_bp_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long tipsLen, float tip_drop_ratio, long long stops_threshold,
@@ -13192,26 +13243,19 @@ bub_label_t* b_mask_t)
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic;
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1);
// print_untig_by_read(copy_ug, "m64011_190830_220126/175638789/ccs", 1369536, NULL, NULL, "sa");
// print_untig_by_read(copy_ug, "m64012_190921_234837/21039588/ccs", 5097804, NULL, NULL, "sa");
// print_untig_by_read(copy_ug, "m64011_190830_220126/88867583/ccs", 603738, NULL, NULL, "sa");
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);
// print_untig_by_read(copy_ug, "m64011_190830_220126/175638789/ccs", 1369536, NULL, NULL, "sb");
// print_untig_by_read(copy_ug, "m64012_190921_234837/21039588/ccs", 5097804, NULL, NULL, "sb");
// print_untig_by_read(copy_ug, "m64011_190830_220126/88867583/ccs", 603738, NULL, NULL, "sb");
// print_r_het(cov, R_INF.trio_flag, "out-0");
set_trio_flag_by_cov(ug, sg, cov);
// print_r_het(cov, R_INF.trio_flag, "out-1");
@@ -23387,7 +23431,6 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, trans_chain* t_ch)
}
}
///fprintf(stderr, "keep_atg: %u\n", keep_atg);
ma_ug_destroy(atg);
}
@@ -23404,10 +23447,7 @@ uint32_t collect_p_trans)
ma_utg_t* u = NULL;
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources,
coverage_cut, max_hang, min_ovlp, (asm_opt.purge_level_primary>0||i_cov)?1:0);
if(cov->t_ch)
{
set_r_het_flag(*ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
}
if(cov->t_ch) set_r_het_flag(*ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex, b_mask_t);
@@ -23426,7 +23466,7 @@ uint32_t collect_p_trans)
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
if(i_cov) goto skip_purge;
if(i_cov && collect_p_trans == 0) goto skip_purge;
if(asm_opt.purge_level_primary > 0)
{
@@ -23435,7 +23475,7 @@ uint32_t collect_p_trans)
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_thres, asm_opt.purge_overlap_len, max_hang, min_ovlp, drop_ratio,
just_contain, 0, cov, 0);
just_contain, 0, cov, !!(cov->t_ch&&collect_p_trans));
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -23504,13 +23544,6 @@ uint32_t collect_p_trans)
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
if(i_cov)
{
if(cov->t_ch && collect_p_trans)
{
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_thres, asm_opt.purge_overlap_len, max_hang, min_ovlp, drop_ratio,
0, 0, cov, collect_p_trans);
}
(*i_cov) = cov;
}
else