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improve speed

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This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
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Process_Read.h
+17 -4
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@@ -14,9 +14,11 @@
#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.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(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + 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]
@@ -61,10 +63,20 @@ int get_read(kseq_t *s);
typedef struct
{
uint64_t** N_site;
uint8_t* read;
///uint8_t* read;
char* name;
uint64_t* index;
uint8_t** read_sperate;
uint64_t* read_length;
///seq start pos in uint8_t* read
///do not need it
///uint64_t* index;
uint64_t index_size;
///name start pos in char* name
uint64_t* name_index;
uint64_t name_index_size;
uint64_t total_reads;
@@ -100,6 +112,7 @@ typedef struct
char* seq;
long long length;
long long size;
long long RID;
} UC_Read;
void init_R_buffer(int thread_num);