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Reduce memory requirement

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This commit is contained in:
Haoyu Cheng
2019-05-16 00:22:20 -04:00
parent 45355a1103
commit 3c5799aa1b
12 changed files with 320 additions and 39 deletions
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Process_Read.h
+44 -3
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@@ -16,13 +16,41 @@
#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_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])
#define Get_NAME(R_INF, ID) (R_INF.name + R_INF.name_index[ID])
#define Get_READ(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + ID
#define Get_NAME(R_INF, ID) R_INF.name + R_INF.name_index[ID]
KSEQ_INIT(gzFile, gzread)
static uint8_t seq_nt6_table[256] = {
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
};
static char bit_t_seq_table[256][4] = {0};
static char s_H[4] = {'A', 'C', 'G', 'T'};
static char rc_Table[4] = {'T', 'G', 'C', 'A'};
#define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
void init_kseq(char* file);
void destory_kseq();
int get_read(kseq_t *s);
@@ -31,7 +59,8 @@ int get_read(kseq_t *s);
typedef struct
{
char* read;
uint64_t** N_site;
uint8_t* read;
char* name;
uint64_t* index;
uint64_t index_size;
@@ -64,11 +93,23 @@ typedef struct
int all_read_end;
} R_buffer;
typedef struct
{
char* seq;
long long length;
long long size;
} UC_Read;
void init_R_buffer(int thread_num);
void init_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 init_UC_Read(UC_Read* r);
void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
void reverse_complement(char* pattern, uint64_t length);
void Counting_block();
void destory_R_buffer_block(R_buffer_block* curr_sub_block);