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collect contig alignment + renew_utg bug fixed

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chhylp123
2021-05-09 17:47:50 -04:00
parent 03adce6202
commit 7918396d21
7 changed files with 431 additions and 19 deletions
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Overlaps.h
+22
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@@ -1195,6 +1195,28 @@ uint32_t get_u_trans_spec(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t
int ma_ug_seq(ma_ug_t *g, asg_t *read_g, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources,
kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E, uint32_t is_polish);
typedef struct{
ma_sub_t* coverage_cut;
ma_hit_t_alloc* sources;
ma_hit_t_alloc* reverse_sources;
long long tipsLen;
float tip_drop_ratio;
long long stops_threshold;
R_to_U* ruIndex;
float chimeric_rate;
float drop_ratio;
int max_hang;
int min_ovlp;
int is_bench;
bub_label_t* b_mask_t;
}ug_opt_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,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t);
#define JUNK_COV 5
#define DISCARD_RATE 0.8