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https://github.com/chhylp123/hifiasm.git
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124 lines
3.1 KiB
C
124 lines
3.1 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]>>2) + 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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static uint8_t seq_nt6_table[256] = {
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
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};
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static char bit_t_seq_table[256][4] = {0};
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static char s_H[4] = {'A', 'C', 'G', 'T'};
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static char rc_Table[4] = {'T', 'G', 'C', 'A'};
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#define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
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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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uint64_t** N_site;
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uint8_t* 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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typedef struct
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{
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char* seq;
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long long length;
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long long size;
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} UC_Read;
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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 compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
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void init_UC_Read(UC_Read* r);
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void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
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void reverse_complement(char* pattern, uint64_t length);
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void write_All_reads(All_reads* r, char* read_file_name);
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int load_All_reads(All_reads* r, char* read_file_name);
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void destory_All_reads(All_reads* r);
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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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