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checkpoint for scaffolding

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chhylp123
2023-09-15 12:58:34 -04:00
parent 858b95a3bb
commit c7685e6f19
8 changed files with 1735 additions and 98 deletions
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Process_Read.h
+10
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@@ -25,6 +25,7 @@
#define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
#define CHECK_BY_NAME(R_INF, NAME, ID) (Get_NAME_LENGTH((R_INF),(ID))==strlen((NAME)) && \
memcmp((NAME), Get_NAME((R_INF), (ID)), Get_NAME_LENGTH((R_INF),(ID))) == 0)
#define IS_SCAF_READ(R_INF, ID) ((R_INF).read_sperate[(ID)] == NULL)
extern uint8_t seq_nt6_table[256];
extern char bit_t_seq_table[256][4];
@@ -204,6 +205,13 @@ typedef struct
// uint32_t mm;
} all_ul_t;
typedef struct {
ul_vec_t *a;
size_t n, m;
uint8_t dd;
} scaf_res_t;
extern all_ul_t UL_INF;
extern all_ul_t ULG_INF;
// extern uint32_t *het_cnt;
@@ -239,5 +247,7 @@ uint64_t retrieve_r_cov_region(const ul_idx_t *ul, uint64_t id, uint8_t strand,
void append_ul_t_back(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on, float p_chain_rate);
void write_compress_base_disk(FILE *fp, uint64_t ul_rid, char *str, uint32_t len, ul_vec_t *buf);
int64_t load_compress_base_disk(FILE *fp, uint64_t *ul_rid, char *dest, uint32_t *len, ul_vec_t *buf);
scaf_res_t *init_scaf_res_t(uint32_t n);
void destroy_scaf_res_t(scaf_res_t *p);
#endif