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fixed gap filling with UL

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chhylp123
2022-11-25 11:46:37 -05:00
parent 979d83f68d
commit fc76af1285
6 changed files with 760 additions and 182 deletions
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Overlaps.h
+16
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@@ -1077,6 +1077,20 @@ typedef struct{
uint64_t* readLen;
}ug_opt_t;
typedef struct{
ma_hit_t_alloc **src;
ma_hit_t_alloc **r_src;
long long *n_read;
uint64_t **readLen;
asg_t **sg;
R_to_U *ruIndex;
ma_sub_t **cov;
bub_label_t *b_mask_t;
int64_t max_hang;
int64_t mini_ovlp;
}ul_renew_t;
void adjust_utg_by_trio(ma_ug_t **ug, asg_t* read_g, uint8_t flag, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
long long tipsLen, float tip_drop_ratio, long long stops_threshold,
@@ -1145,6 +1159,8 @@ void set_reverse_overlap(ma_hit_t* dest, ma_hit_t* source);
// void break_ug_contig(ma_ug_t **ug, asg_t *read_g, All_reads *RNF, ma_sub_t *coverage_cut,
// ma_hit_t_alloc* sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp,
// int* b_low_cov, int* b_high_cov, double m_rate);
void ma_hit_contained_advance(ma_hit_t_alloc* sources, long long n_read, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp);
#define JUNK_COV 5
#define DISCARD_RATE 0.8