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chhylp123
2020-12-17 02:53:31 -05:00
parent 73b5ef6769
commit f3e390eee8
7 changed files with 1362 additions and 223 deletions
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Overlaps.h
+39
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@@ -1064,6 +1064,45 @@ uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, int max_
uint32_t positive_flag, uint32_t negative_flag, uint32_t is_pop);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
typedef struct{
double weight;
uint32_t uID:31, del:1;
uint64_t dis;
///uint32_t enzyme;
} hc_edge;
typedef struct{
kvec_t(hc_edge) e;
kvec_t(hc_edge) f;//forbiden
} hc_linkeage;
typedef struct{
kvec_t(hc_linkeage) a;
kvec_t(uint64_t) enzymes;
uint32_t* u_idx;
} hc_links;
typedef struct{
///kvec_t(hc_edge) a;
size_t n, m;
hc_edge *a;
}hc_edge_warp;
void clean_primary_untig_graph(ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources,
long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, buf_t* b_0, uint8_t* visit, float density, uint32_t miniHapLen,
uint32_t miniBiGraph, float chimeric_rate, int is_final_clean, int just_bubble_pop,
float drop_ratio, hc_links* link);
void adjust_utg_by_primary(ma_ug_t **ug, asg_t* read_g, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
long long bubble_dist, 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, hc_links* link);
void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug);
#define JUNK_COV 5
#define DISCARD_RATE 0.8