1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
|
/*
This file is a part of KMC software distributed under GNU GPL 3 licence.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
Authors: Marek Kokot
Version: 2.3.0
Date : 2015-08-21
*/
#ifndef _FASTQ_READER_H
#define _FASTQ_READER_H
#include "defs.h"
#include "queues.h"
#include "config.h"
#include <stdio.h>
#include <iostream>
#include <zlib.h>
#include <bzlib.h>
using namespace std;
//************************************************************************************************************
// FASTA/FASTQ reader class
//************************************************************************************************************
class CFastqReader {
typedef enum {m_plain, m_gzip, m_bzip2} t_mode;
CMemoryPool *pmm_fastq;
string input_file_name;
CFilteringParams::file_type file_type;
int kmer_len;
t_mode mode;
FILE *in;
gzFile_s *in_gzip;
BZFILE *in_bzip2;
int bzerror;
uint64 part_size;
uchar *part;
uint64 part_filled;
uint32 gzip_buffer_size;
uint32 bzip2_buffer_size;
bool SkipNextEOL(uchar *part, int64 &pos, int64 max_pos);
bool IsEof();
public:
CFastqReader(CMemoryPool *_pmm_fastq, CFilteringParams::file_type _file_type, uint32 _gzip_buffer_size, uint32 _bzip2_buffer_size, int _kmer_len);
~CFastqReader();
static uint64 OVERHEAD_SIZE;
bool SetNames(string _input_file_name);
bool SetPartSize(uint64 _part_size);
bool OpenFiles();
bool GetPart(uchar *&_part, uint64 &_size);
};
//************************************************************************************************************
// Wrapper for FASTA/FASTQ reader class - for multithreading purposes
//************************************************************************************************************
class CWFastqReader {
CMemoryPool *pmm_fastq;
CFastqReader *fqr;
string file_name;
uint64 part_size;
CInputFilesQueue *input_files_queue;
CPartQueue *part_queue;
CFilteringParams::file_type file_type;
uint32 gzip_buffer_size;
uint32 bzip2_buffer_size;
int kmer_len;
public:
CWFastqReader(CFilteringParams &Params, CFilteringQueues &Queues);
~CWFastqReader();
void operator()();
};
#endif
// ***** EOF
|
