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debug ul

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chhylp123
2021-10-10 13:37:32 -04:00
parent 7dd4a848b9
commit cb320b88f3
7 changed files with 1212 additions and 325 deletions
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152
Overlaps.cpp
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@@ -15,6 +15,7 @@
#include "Assembly.h"
#include "rcut.h"
#include "horder.h"
#include "inter.h"
uint32_t debug_purge_dup = 0;
@@ -13280,6 +13281,151 @@ long long gap_fuzz, bub_label_t* b_mask_t)
}
}
void print_debug_gfa(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)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
sprintf(gfa_name, "%s.after.clean_d_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
free(gfa_name);
}
void output_ul_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,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
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;
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;
opt.gap_fuzz = gap_fuzz;
kvec_asg_arc_t_warp new_rtg_edges, d_edges;
kv_init(new_rtg_edges.a); kv_init(d_edges.a);
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges, 1);///polish
print_debug_gfa(ug, sg, coverage_cut, output_file_name, sources, ruIndex);
ul_resolve(ug, asm_opt.polyploidy);
/**
hap_cov_t *cov = NULL;
trans_chain* t_ch = NULL;
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_trans(output_file_name);
if(!t_ch)
{
new_rtg_edges.a.n = 0;
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, 0);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
if(asm_opt.is_alt)
{
output_contig_graph_alternative(copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp);
}
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);
new_rtg_edges.a.n = 0;
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov->t_ch);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
}
// char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
// sprintf(gfa_name, "%s.pre.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);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch, &opt, 0, asm_opt.scffold?&rhits:NULL);
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);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
asg_arc_t* av = NULL;
uint32_t v, w, k, i, nv;
for (i = 0; i < d_edges.a.n; i++)
{
v = d_edges.a.a[i].ul>>32;
w = d_edges.a.a[i].v;
av = asg_arc_a(sg, v);
nv = asg_arc_n(sg, v);
for (k = 0; k < nv; k++)
{
if(av[k].del) continue;
if(av[k].v == w)
{
av[k].del = 1;
break;
}
}
}
kv_destroy(d_edges.a);
asg_cleanup(sg);
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);
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, NULL);
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, NULL);
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,
int max_hang, int min_ovlp, R_to_U* ruIndex, bub_label_t* b_mask_t)
{
@@ -30974,6 +31120,12 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
output_poly_trio(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, asm_opt.polyploidy);
}
else if(asm_opt.ar)
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_ul_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, gap_fuzz, &b_mask_t);
}
else if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;