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purge_dups for high het

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chhylp123
2021-03-08 20:52:11 -05:00
parent e8b92f7a40
commit 8aa87fdce8
8 changed files with 2766 additions and 1765 deletions
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Overlaps.h
+33 -10
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@@ -478,7 +478,6 @@ void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig, uint8
void get_R_to_U(R_to_U* x, uint32_t rID, uint32_t* uID, uint32_t* is_Unitig);
void transfor_R_to_U(R_to_U* x);
void debug_utg_graph(ma_ug_t *ug, asg_t* read_g, kvec_asg_arc_t_warp* edge, int require_equal_nv, int test_tangle);
int asg_pop_bubble_primary(asg_t *g, int max_dist);
long long asg_arc_del_simple_circle_untig(ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, asg_t *g, long long circleLen, int is_drop);
typedef struct {
@@ -493,9 +492,35 @@ typedef struct {
uint32_t new_edges_i;
} Edge_iter;
typedef struct {
asg_arc_t x;
uint64_t Off;
uint64_t weight;
}asg_arc_t_offset;
typedef struct {
kvec_t(asg_arc_t_offset) a;
uint64_t i;
}kvec_asg_arc_t_offset;
typedef struct {
uint32_t n;
uint32_t* cov;
uint64_t* pos_idx;
ma_hit_t_alloc* reverse_sources;
ma_sub_t *coverage_cut;
R_to_U* ruIndex;
asg_t *read_g;
int max_hang;
int min_ovlp;
kvec_asg_arc_t_offset u_buffer;
kvec_t_i32_warp tailIndex;
kvec_t_i32_warp prevIndex;
}hap_cov_t;
void init_Edge_iter(asg_t* g, uint32_t v, asg_arc_t* new_edges, uint32_t new_edges_n, Edge_iter* x);
int get_arc_t(Edge_iter* x, asg_arc_t* get);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, int max_dist, uint32_t positive_flag, uint32_t negative_flag);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, int max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov);
inline int get_real_length(asg_t *g, uint32_t v, uint32_t* v_s)
@@ -1040,10 +1065,10 @@ R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t bac
uint32_t is_bubble_check, uint32_t is_primary_check);
uint32_t get_edge_from_source(ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t query, uint32_t target, asg_arc_t* t);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, int max_dist, buf_t *b,
uint32_t positive_flag, uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, int max_dist, buf_t *b, uint32_t positive_flag,
uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes, hap_cov_t *cov);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
void asg_bub_backtrack_primary(asg_t *g, uint32_t v0, buf_t *b);
typedef struct{
double weight;
@@ -1084,11 +1109,6 @@ typedef struct{
void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num);
void destory_hc_links(hc_links* link);
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,
@@ -1112,6 +1132,9 @@ inline int inter_interval(int a_s, int a_e, int b_s, int b_e, int* i_s, int* i_e
return 1;
}
#define JUNK_COV 5
#define DISCARD_RATE 0.8