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for v0.14

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chhylp123
2021-02-09 13:00:23 -05:00
parent fda13cb0e4
commit 8467d58ef1
7 changed files with 2928 additions and 925 deletions
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hic.h
+24 -1
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@@ -14,6 +14,21 @@ void push_hc_edge(hc_linkeage* x, uint64_t uID, double weight, int dir, uint64_t
void hic_analysis(ma_ug_t *ug, asg_t* read_g, hc_links* link);
void hic_benchmark(ma_ug_t *ug, asg_t* read_g);
typedef struct {
double w;
uint32_t id, occ;
///uint32_t *bid, bid_n;
ma_utg_t *u;
uint64_t l_d, r_d;
}chain_hic_w_type;
typedef struct {
size_t n, m;
chain_hic_w_type* a;
uint32_t max_bub_id;
uint32_t *chain_idx, u_n;
}chain_hic_warp;
typedef struct {
long long g_occ, b_occ;
uint64_t id;
@@ -27,11 +42,12 @@ typedef struct {
kvec_t(uint32_t) num;
kvec_t(uint64_t) pathLen;
kvec_t(uint64_t) b_s_idx;
uint64_t s_bub, f_bub, b_bub, b_end_bub, tangle_bub, cross_bub;
uint64_t s_bub, f_bub, b_bub, b_end_bub, tangle_bub, cross_bub, mess_bub;
uint32_t check_het;
asg_t *b_g;
ma_ug_t* b_ug;
kvec_t(chain_w_type) chain_weight;
chain_hic_warp c_w;
} bubble_type;
#define P_het(B) ((B).num.n)
#define M_het(B) ((B).num.n + 1)
@@ -45,5 +61,12 @@ typedef struct {
void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t* sink, uint32_t** a, uint32_t* n, uint64_t* pathBase);
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, hc_links* link);
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);
#endif