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UL graph with graph cleaning

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chhylp123
2022-08-02 15:48:16 -04:00
parent 91de382bde
commit 89e0d1aafa
4 changed files with 1746 additions and 109 deletions
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Overlaps.cpp
+18 -7
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@@ -14818,7 +14818,7 @@ 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, int is_polish, int is_update_ou, int is_check_alter_lable)
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, int is_update_ou, int is_check_alter_lable, int is_seq)
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
@@ -14844,13 +14844,24 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, int is_pol
}
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);
if(is_seq) {
ma_ug_seq(ug, read_g, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 0);
}
// 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);
sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, read_g, coverage_cut, sources, ruIndex, "utg", output_file);
char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
FILE* output_file = NULL;
if(is_seq) {
sprintf(gfa_name, "%s.r_utg.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print(ug, read_g, coverage_cut, sources, ruIndex, "utg", output_file);
} else {
sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, read_g, coverage_cut, sources, ruIndex, "utg", output_file);
}
fclose(output_file);
free(gfa_name);
@@ -31552,7 +31563,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
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);
// 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");