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fix bug for broken bubbles

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chhylp123
2021-01-15 07:33:13 -05:00
parent 88f5b11f04
commit a009026e65
6 changed files with 3441 additions and 359 deletions
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hic.h
+15 -2
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@@ -10,10 +10,16 @@
#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, int weight, int dir, uint64_t* d);
void 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, hc_links* link);
void hic_benchmark(ma_ug_t *ug, asg_t* read_g);
typedef struct {
long long g_occ, b_occ;
uint64_t id;
uint8_t del;
}chain_w_type;
typedef struct {
uint32_t* index;
ma_ug_t* ug;
@@ -21,8 +27,13 @@ typedef struct {
kvec_t(uint32_t) num;
kvec_t(uint64_t) pathLen;
kvec_t(uint64_t) b_s_idx;
uint64_t f_bub, b_bub;
uint64_t s_bub, f_bub, b_bub;
uint32_t check_het;
asg_t *b_g;
uint32_t *b_g_index;
ma_ug_t* b_ug;
uint32_t *b_ug_index;
kvec_t(chain_w_type) chain_weight;
} bubble_type;
#define P_het(B) ((B).num.n)
#define M_het(B) ((B).num.n + 1)
@@ -34,5 +45,7 @@ typedef struct {
#define IF_HOM(ID, B) ((B).index[(ID)] > (B).f_bub+1)
#define Get_bub_num(RECORD) ((RECORD).num.n-1)
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);
#endif