xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-09 09:28:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

update for low coverge data

Browse Source
This commit is contained in:
chhylp123
2024-12-16 06:25:31 -05:00
parent 4889f1c6d8
commit 3067771783
8 changed files with 1073 additions and 154 deletions
Download Patch File Download Diff File Expand all files Collapse all files
gfa_ut.h
+2 -2
View File
@@ -16,7 +16,7 @@ typedef struct {
} sset_aux;
void ul_clean_gfa(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, char *o_file);
double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, uint8_t *cmk, char *o_file);
uint32_t asg_arc_cut_tips(asg_t *g, uint32_t max_ext, asg64_v *in, uint32_t is_ou, R_to_U *ru, telo_end_t *te);
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, telo_end_t *te);
void asg_arc_cut_chimeric(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_t ou_thres, telo_end_t *te);
@@ -33,7 +33,7 @@ void recover_contain_g(asg_t *g, ma_hit_t_alloc *src, R_to_U* ruIndex, int64_t m
void normalize_gou(asg_t *g);
void prt_specfic_sge(asg_t *g, uint32_t src, uint32_t dst, const char* cmd);
asg_t *gen_ng(ma_ug_t *ug, asg_t *sg, ug_opt_t *uopt, ma_sub_t **cov, R_to_U *ruI, uint64_t scaffold_len);
void post_rescue(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, bub_label_t *b_mask_t, long long no_trio_recover);
void post_rescue(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, bub_label_t *b_mask_t, long long no_trio_recover, uint8_t *cmk);
// void print_raw_u2rgfa_seq(all_ul_t *aln, R_to_U* rI, uint32_t is_detail);
bubble_type *gen_bubble_chain(asg_t *sg, ma_ug_t *ug, ug_opt_t *uopt, uint8_t **ir_het, uint8_t avoid_het);
void filter_sg_by_ug(asg_t *rg, ma_ug_t *ug, ug_opt_t *uopt);