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avoid misassemblies; better polyploidy graph

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chhylp123
2023-03-22 12:23:53 -04:00
parent d4773a497f
commit 86b7dd424a
12 changed files with 1931 additions and 79 deletions
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gfa_ut.h
+1 -1
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@@ -22,7 +22,7 @@ void asg_iterative_semi_circ(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_
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, 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, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len);
uint32_t is_topo, uint32_t min_diff, uint32_t min_ou, 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 min_diff);