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write to hifiasm read store

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Heng Li
2020-03-26 14:23:17 -04:00
parent c3bbaa8a39
commit 0dd927bdce
8 changed files with 91 additions and 67 deletions
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16
Process_Read.h
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@@ -18,11 +18,11 @@
#define IS_FULL(buffer) ((buffer.num >= buffer.size)?1:0)
#define IS_EMPTY(buffer) ((buffer.num == 0)?1:0)
///#define Get_READ_LENGTH(R_INF, ID) (R_INF.index[ID+1] - R_INF.index[ID])
#define Get_READ_LENGTH(R_INF, ID) R_INF.read_length[(ID)]
#define Get_NAME_LENGTH(R_INF, ID) (R_INF.name_index[(ID)+1] - R_INF.name_index[(ID)])
#define Get_READ_LENGTH(R_INF, ID) (R_INF).read_length[(ID)]
#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_NAME(R_INF, ID) R_INF.name + R_INF.name_index[(ID)]
#define Get_READ(R_INF, ID) (R_INF).read_sperate[(ID)]
#define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
KSEQ_INIT(gzFile, gzread)
@@ -139,8 +139,6 @@ typedef struct
extern All_reads R_INF;
void malloc_All_reads(All_reads* r);
typedef struct
{
kseq_t* read;
@@ -175,10 +173,12 @@ typedef struct
void init_R_buffer(int thread_num);
void init_All_reads(All_reads* r);
void malloc_All_reads(All_reads* r);
void* input_reads_muti_threads(void*);
void init_R_buffer_block(R_buffer_block* curr_sub_block);
int get_reads_mul_thread(R_buffer_block* curr_sub_block);
void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
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 init_UC_Read(UC_Read* r);
void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID);
@@ -196,6 +196,4 @@ void clear_R_buffer();
void init_gz_files(hifiasm_opt_t* asm_opt);
void destory_gz_files();
void ha_insert_read_len(All_reads *r, int read_len, int name_len);
#endif