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UL_gdp

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chhylp123
2022-04-13 16:15:03 -04:00
parent 75f8048b18
commit 9c79bdfe7f
10 changed files with 1860 additions and 267 deletions
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Overlaps.h
+13
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@@ -225,6 +225,16 @@ typedef struct {
kvec_t(uint64_t) interval;
} ucov_t;
typedef struct {
uint32_t u, off, pos;
} utg_rid_dt;
typedef struct {
uint32_t *idx;
kvec_t(utg_rid_dt) p;
asg_t *rg;
} utg_rid_t;
typedef struct {
kvec_t(uint64_t) idx;
kvec_t(utg_ct_t) rids;
@@ -242,6 +252,7 @@ typedef struct {
ucov_t *cc;
ucov_t *cr;
ul_contain *ct;
utg_rid_t *r_ug;
// cvert_t *nug;
// kv_ul_ov_t *ov;
} ul_idx_t;
@@ -1059,6 +1070,8 @@ int asg_topocut_aux(asg_t *g, uint32_t v, int max_ext);
int asg_arc_del_triangular_directly(asg_t *g, long long min_edge_length,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
int asg_arc_del_short_diploid_by_exact(asg_t *g, int max_ext, ma_hit_t_alloc* sources);
uint32_t print_debug_gfa(asg_t *read_g, ma_ug_t *ug, ma_sub_t* coverage_cut, const char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp);
#define JUNK_COV 5
#define DISCARD_RATE 0.8