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fix bubble popping bugs

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chhylp123
2023-01-15 22:29:20 -05:00
parent 2bf5119bb5
commit 46391eba26
3 changed files with 456 additions and 7 deletions
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horder.cpp
+4 -2
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@@ -31,7 +31,8 @@ KRADIX_SORT_INIT(osg, osg_arc_t, osg_arc_key, member_size(osg_arc_t, u))
#define BREAK_THRES 5000000
#define BREAK_CUTOFF 0.1
#define BREAK_BOUNDARY 0.015
void reduce_hamming_error_adv(ma_ug_t *iug, asg_t *sg, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
int max_hang, int min_ovlp, long long gap_fuzz, bubble_type* bub);
typedef struct {
uint64_t ruid;
@@ -3962,7 +3963,8 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt,
t_idx = init_trans_col(i_ug, h->r_g->n_seq, ref);
// output_hic_rtg(i_ug, h->r_g, opt, asm_opt.output_file_name);
reduce_hamming_error(h->r_g, opt->sources, opt->coverage_cut, opt->max_hang, opt->min_ovlp, opt->gap_fuzz);
// reduce_hamming_error(h->r_g, opt->sources, opt->coverage_cut, opt->max_hang, opt->min_ovlp, opt->gap_fuzz);
reduce_hamming_error_adv(NULL, h->r_g, opt->sources, opt->coverage_cut, opt->max_hang, opt->min_ovlp, opt->gap_fuzz, NULL);
/**
scaffold_hap(h, t_idx, opt, round, asm_opt.output_file_name, FATHER);
scaffold_hap(h, t_idx, opt, round, asm_opt.output_file_name, MOTHER);