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chhylp123
2022-07-24 18:13:16 -04:00
parent 138610b049
commit 33afa25398
5 changed files with 3581 additions and 41 deletions
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Overlaps.h
+3 -1
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@@ -259,6 +259,7 @@ typedef struct {
// kv_ul_ov_t *ov;
} ul_idx_t;
#define MA_HT_DOUBLE (-1024)
#define MA_HT_INT (-1)
#define MA_HT_QCONT (-2)
#define MA_HT_TCONT (-3)
@@ -1079,7 +1080,7 @@ 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);
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, int is_polish, int is_update_ou, int is_check_alter_lable);
void debug_info_of_specfic_node(const char* name, asg_t *g, R_to_U* ruIndex, const char* command);
ma_ug_t *gen_polished_ug(const ug_opt_t *uopt, asg_t *sg);
void output_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
@@ -1087,6 +1088,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp);
void flat_soma_v(asg_t *sg, ma_hit_t_alloc* sources, R_to_U* ruIndex);
void hic_clean(asg_t* read_g);
int64_t count_edges_v_w(asg_t *g, uint32_t v, uint32_t w);
void renew_utg(ma_ug_t **ug, asg_t* read_g, kvec_asg_arc_t_warp* edge);
#define JUNK_COV 5
#define DISCARD_RATE 0.8