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chhylp123
2024-11-12 23:53:29 -05:00
parent 6de4e14782
commit 80fa5ed436
11 changed files with 1211 additions and 135 deletions
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18
Process_Read.h
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@@ -22,6 +22,7 @@
#define Get_NAME_LENGTH(R_INF, ID) ((R_INF).name_index[(ID)+1] - (R_INF).name_index[(ID)])
///#define Get_READ(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + ID
#define Get_READ(R_INF, ID) (R_INF).read_sperate[(ID)]
#define Get_QUAL(R_INF, ID) (R_INF).rsc[(ID)]
#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)
@@ -38,6 +39,8 @@ extern char rc_Table[6];
void init_aux_table();
typedef struct { size_t n, m; uint8_t *a; } asg8_v;
typedef struct
{
uint64_t x_id;
@@ -119,6 +122,7 @@ typedef struct
uint64_t* read_length;
uint64_t* read_size;
uint8_t* trio_flag;
uint8_t** rsc;
///seq start pos in uint8_t* read
///do not need it
@@ -223,6 +227,7 @@ void init_All_reads(All_reads* r);
void malloc_All_reads(All_reads* r);
void ha_insert_read_len(All_reads *r, int read_len, int name_len);
void ha_compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
void ha_compress_qual(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitn, uint64_t sc_off);
void init_UC_Read(UC_Read* r);
void recover_UC_Read(UC_Read* r, const All_reads *R_INF, uint64_t ID);
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID);
@@ -254,4 +259,17 @@ scaf_res_t *init_scaf_res_t(uint32_t n);
void destroy_scaf_res_t(scaf_res_t *p);
void read_ma(ma_hit_t* x, FILE* fp);
const uint64_t sc_tb[8] = {
10, 20, 30, 40, 50, 60, 70, 80
};
#define sc_bn 2
#define sc_bm ((((uint64_t)1)<<sc_bn)-1)
#define sc_wn 5
void convert_qual(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitu, uint64_t rev, uint64_t sc_off);
int64_t retrive_bqual(asg8_v *dv, uint8_t *ds, uint64_t id, int64_t s, int64_t e, uint8_t rev, int64_t bitn);
void print_fastq(FILE *fp, char *id, char *bs, char *qual, uint64_t bitu, uint64_t sc_off);
void ha_compress_qual_bit(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitn);
#endif