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update trans chain

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chhylp123
2021-03-10 22:46:50 -05:00
parent 8aa87fdce8
commit 4c2ce6fc6b
6 changed files with 1363 additions and 334 deletions
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Overlaps.h
+33 -17
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@@ -503,24 +503,10 @@ typedef struct {
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, hap_cov_t *cov);
inline int get_real_length(asg_t *g, uint32_t v, uint32_t* v_s)
@@ -1065,8 +1051,6 @@ 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, 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);
@@ -1101,6 +1085,31 @@ typedef struct{
uint64_t r_num;
} hc_links;
typedef struct{
kvec_t(uint32_t) uIDs;
kvec_t(uint32_t) idx;
uint32_t chain_num;
uint32_t* u_idx;
uint64_t r_num;
}trans_chain;
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;
hc_links* link;
///trans_chain t_ch;
}hap_cov_t;
typedef struct{
///kvec_t(hc_edge) a;
size_t n, m;
@@ -1109,6 +1118,10 @@ typedef struct{
void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num);
void destory_hc_links(hc_links* link);
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);
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);
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,
@@ -1124,6 +1137,9 @@ asg_t* copy_read_graph(asg_t *src);
ma_ug_t *ma_ug_gen(asg_t *g);
void ma_ug_destroy(ma_ug_t *ug);
inline int inter_interval(int a_s, int a_e, int b_s, int b_e, int* i_s, int* i_e)
{
if(a_s > b_e || b_s > a_e) return 0;