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chhylp123
2022-07-24 18:13:16 -04:00
parent 138610b049
commit 33afa25398
5 changed files with 3581 additions and 41 deletions
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Overlaps.cpp
+10 -8
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@@ -11180,7 +11180,6 @@ void debug_contig_end(ma_ug_t *ug, asg_t* read_g, kvec_asg_arc_t_warp* edge)
}
}
void renew_utg(ma_ug_t **ug, asg_t* read_g, kvec_asg_arc_t_warp* edge);
void push_sub_unitig(ma_ug_t *n_ug, ma_utg_t *src_u, asg_t *read_g, kvec_asg_arc_t_warp* edge,
uint32_t beg_idx, uint32_t occ)
{
@@ -14819,14 +14818,14 @@ const char* command)
uint32_t print_debug_gfa(asg_t *read_g, ma_ug_t *ug, ma_sub_t* coverage_cut, const char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, int is_polish, int is_update_ou, int is_check_alter_lable)
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
if(ug == NULL) {
ug = ma_ug_gen(read_g);
} else {
} else if(is_check_alter_lable) {
uint32_t i;
for (i = 0; i < ug->u.n; ++i)
{
@@ -14844,8 +14843,8 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
}
}
update_ug_ou(ug, read_g);
ma_ug_seq(ug, read_g, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 0);
if(is_update_ou) update_ug_ou(ug, read_g);
if(is_polish) ma_ug_seq(ug, read_g, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 0);
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -16627,7 +16626,7 @@ int min_ovlp, hap_cov_t *cov)
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, cov->is_r_het, (uint32_t)-1, drop_ratio);
drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex, cov->is_r_het);
print_debug_gfa(read_g, ug, coverage_cut, "debug_clean_end", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
// print_debug_gfa(read_g, ug, coverage_cut, "debug_clean_end", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
unitig_arc_del_short_diploid_by_length_topo(g, ug, drop_ratio, asm_opt.max_short_tip, reverse_sources, 0, 1);
if(round > 0)
@@ -31549,8 +31548,11 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
gen_ug_opt_t(&uopt, sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex,
(asm_opt.max_short_tip*2), 0.15, 3, 0.05, 0.9, &b_mask_t);
}
if(asm_opt.ar) ul_realignment_gfa(&uopt, sg);
print_debug_gfa(sg, NULL, coverage_cut, "UL.debug", sources, ruIndex, max_hang_length, mini_overlap_length);
if(asm_opt.ar) {
ul_realignment_gfa(&uopt, sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, &b_mask_t, ha_opt_triobin(&asm_opt));
}
print_debug_gfa(sg, NULL, coverage_cut, "UL.debug", sources, ruIndex, max_hang_length, mini_overlap_length, 0, 0, 0);
/**
asg_cut_tip(sg, asm_opt.max_short_tip);
///debug_info_of_specfic_node("m64043_200505_112554/8849050/ccs", sg, "inner_1");