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chhylp123
2021-04-01 21:02:57 -04:00
parent 0605aa1961
commit 46e899bbae
11 changed files with 1494 additions and 401 deletions
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Purge_Dups.h
+28 -1
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@@ -13,6 +13,33 @@
#define REAL_ALTER_THRES 0.1
#define CHAIN_FILTER_RATE 0.7
typedef struct {
uint8_t rev;
uint8_t type;
uint8_t status;
uint32_t x_beg_pos;
uint32_t x_end_pos;
uint32_t y_beg_pos;
uint32_t y_end_pos;
uint32_t x_beg_id;
uint32_t x_end_id;
uint32_t y_beg_id;
uint32_t y_end_id;
uint32_t xUid;
uint32_t yUid;
uint32_t weight;
long long score;
}hap_overlaps;
typedef struct {
kvec_t(hap_overlaps) a;
}kvec_hap_overlaps;
typedef struct {
kvec_hap_overlaps* x;
uint32_t num;
}hap_overlaps_list;
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
@@ -25,6 +52,6 @@ hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R
ma_sub_t *coverage_cut, int max_hang, int min_ovlp, uint32_t is_collect_trans);
void destory_hap_cov_t(hap_cov_t **x);
void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
#endif