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keep long range information

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chhylp123
2021-04-20 01:29:15 -04:00
parent 39c19618e8
commit 475ebb8075
4 changed files with 465 additions and 426 deletions
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hic.h
+2 -3
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@@ -10,7 +10,7 @@
#define RC_2 2
hc_edge* get_hc_edge(hc_links* link, uint64_t src, uint64_t dest, uint64_t dir);
void push_hc_edge(hc_linkeage* x, uint64_t uID, double weight, int dir, uint64_t* d);
hc_edge* push_hc_edge(hc_linkeage* x, uint64_t uID, double weight, int dir, uint64_t* d);
void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch);
void hic_benchmark(ma_ug_t *ug, asg_t* read_g);
@@ -67,13 +67,12 @@ void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t* sink, u
int load_hc_links(hc_links* link, const char *fn);
void write_hc_links(hc_links* link, const char *fn);
void destory_bubbles(bubble_type* bub);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_trans_t *ref);
void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub);
uint32_t connect_bub_occ(bubble_type* bub, uint32_t root_id, uint32_t check_het);
void get_bub_id(bubble_type* bub, uint32_t root, uint64_t* id0, uint64_t* id1, uint32_t check_het);
void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end);
void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ);
uint32_t get_unitig_het_arb(ma_utg_t* u, uint8_t *r_het_flag, uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label);
void debug_gfa_space(ma_ug_t* ug, hap_cov_t *cov);
#endif