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better resolution for complex regions

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chhylp123
2023-02-27 09:35:50 -05:00
parent 04f660fd8c
commit a0f2f70d91
5 changed files with 245 additions and 40 deletions
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gfa_ut.h
+3 -3
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@@ -19,12 +19,12 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
uint32_t asg_arc_cut_tips(asg_t *g, uint32_t max_ext, asg64_v *in, uint32_t is_ou, R_to_U *ru);
void asg_iterative_semi_circ(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_t normal_len, uint32_t pop_chimer, asg64_v *dbg);
void asg_arc_cut_chimeric(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_t ou_thres);
void asg_arc_cut_inexact(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, int32_t max_ext, uint32_t is_ou, uint32_t is_trio, float ou_rat/**, asg64_v *dbg**/);
void asg_arc_cut_inexact(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, int32_t max_ext, uint32_t is_ou, uint32_t is_trio, uint32_t min_diff, float ou_rat/**, asg64_v *dbg**/);
void asg_arc_cut_length(asg_t *g, asg64_v *in, int32_t max_ext, float len_rat, float ou_rat, uint32_t is_ou, uint32_t is_trio,
uint32_t is_topo, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len);
uint32_t is_topo, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len);
void asg_arc_cut_bub_links(asg_t *g, asg64_v *in, float len_rat, float sec_len_rat, float ou_rat, uint32_t is_ou, uint64_t check_dist, ma_hit_t_alloc *rev, R_to_U* rI, int32_t max_ext);
void asg_arc_cut_complex_bub_links(asg_t *g, asg64_v *in, float len_rat, float ou_rat, uint32_t is_ou, bub_label_t *b_mask_t);
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_large_indel(asg_t *g, asg64_v *in, int32_t max_ext, float ou_rat, uint32_t is_ou, uint32_t min_diff);
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, uint64_t is_bridg, uint64_t deep_clean);