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508 —> futhur graph cleaning

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chhylp123
2023-02-12 22:49:12 -05:00
parent 1166b92eb4
commit f2da12a2ad
13 changed files with 4422 additions and 110 deletions
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gfa_ut.h
+1 -1
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@@ -27,7 +27,7 @@ void asg_arc_cut_complex_bub_links(asg_t *g, asg64_v *in, float len_rat, float o
uint32_t asg_cut_large_indel(asg_t *g, asg64_v *in, int32_t max_ext, float ou_rat, uint32_t is_ou);
uint32_t asg_cut_semi_circ(asg_t *g, uint32_t lim_len, uint32_t is_clean);
void ul_realignment_gfa(ug_opt_t *uopt, asg_t *sg, int64_t clean_round, double min_ovlp_drop_ratio,
double max_ovlp_drop_ratio, int64_t max_tip, int64_t max_ul_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file, ul_renew_t *ropt, const char *bin_file, uint64_t free_uld);
double max_ovlp_drop_ratio, int64_t max_tip, int64_t max_ul_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file, ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, uint64_t deep_clean);
void recover_contain_g(asg_t *g, ma_hit_t_alloc *src, R_to_U* ruIndex, int64_t max_hang, int64_t min_ovlp, int64_t ul_occ);
void normalize_gou(asg_t *g);
void prt_specfic_sge(asg_t *g, uint32_t src, uint32_t dst, const char* cmd);