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80 lines
1.5 KiB
C
80 lines
1.5 KiB
C
#ifndef __READ__
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#define __READ__
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#include<stdint.h>
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#include <string.h>
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#include <stdlib.h>
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#include <zlib.h>
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#include "kseq.h"
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#define READ_INIT_NUMBER 1000
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#define READ_BLOCK_SIZE 64
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#define READ_BLOCK_NUM_PRE_THR 100
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#define IS_FULL(buffer) ((buffer.num >= buffer.size)?1:0)
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#define IS_EMPTY(buffer) ((buffer.num == 0)?1:0)
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#define Get_READ_LENGTH(R_INF, ID) (R_INF.index[ID+1] - R_INF.index[ID])
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#define Get_NAME_LENGTH(R_INF, ID) (R_INF.name_index[ID+1] - R_INF.name_index[ID])
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#define Get_READ(R_INF, ID) (R_INF.read + R_INF.index[ID])
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#define Get_NAME(R_INF, ID) (R_INF.name + R_INF.name_index[ID])
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KSEQ_INIT(gzFile, gzread)
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void init_kseq(char* file);
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void destory_kseq();
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int get_read(kseq_t *s);
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typedef struct
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{
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char* read;
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char* name;
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uint64_t* index;
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uint64_t index_size;
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uint64_t* name_index;
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uint64_t name_index_size;
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uint64_t total_reads;
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uint64_t total_reads_bases;
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uint64_t total_name_length;
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} All_reads;
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extern All_reads R_INF;
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void malloc_All_reads(All_reads* r);
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typedef struct
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{
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kseq_t* read;
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long long num;
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} R_buffer_block;
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typedef struct
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{
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R_buffer_block* sub_block;
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long long block_inner_size;
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long long size;
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long long num;
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int all_read_end;
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} R_buffer;
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void init_R_buffer(int thread_num);
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void init_All_reads(All_reads* r);
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void* input_reads_muti_threads(void*);
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void init_R_buffer_block(R_buffer_block* curr_sub_block);
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int get_reads_mul_thread(R_buffer_block* curr_sub_block);
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void Counting_block();
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void destory_R_buffer_block(R_buffer_block* curr_sub_block);
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void destory_R_buffer();
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void clear_R_buffer();
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#endif
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