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chhylp123
2021-05-17 00:12:41 -04:00
parent 2bbac713ef
commit be8e1e3117
5 changed files with 670 additions and 118 deletions
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Overlaps.h
+10
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@@ -27,6 +27,7 @@
#define DOUBLE_CHECK_THRES 0.1
#define FINAL_DOUBLE_CHECK_THRES 0.2
#define CHIMERIC_TRIM_THRES 4
#define GAP_LEN 100
// #define PRIMARY_LABLE 1
// #define ALTER_LABLE 2
// #define HAP_LABLE 4
@@ -1209,6 +1210,7 @@ typedef struct{
int max_hang;
int min_ovlp;
int is_bench;
long long gap_fuzz;
bub_label_t* b_mask_t;
}ug_opt_t;
@@ -1218,6 +1220,14 @@ 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);
uint32_t cmp_untig_graph(ma_ug_t *src, ma_ug_t *dest);
void reduce_hamming_error(asg_t *sg, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
int max_hang, int min_ovlp, long long gap_fuzz);
int ma_ug_seq_scaffold(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);
void ma_ug_print(const ma_ug_t *ug, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, const char* prefix, FILE *fp);
void ma_ug_print_simple(const ma_ug_t *ug, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, const char* prefix, FILE *fp);
#define JUNK_COV 5
#define DISCARD_RATE 0.8