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
|
/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _FastqLoader
#define _FastqLoader
#include "LoaderInterface.h"
#include "ArrayOfReads.h"
#include "Read.h"
#include "BufferedReader.h"
#include <RayPlatform/memory/MyAllocator.h>
#include <fstream>
#include <vector>
#include <sstream>
#include <stdio.h>
#include <string>
using namespace std;
/**
* \author Sébastien Boisvert
*/
class FastqLoader: public LoaderInterface{
BufferedReader m_lineReader;
int m_loaded;
int m_size;
FILE*m_f;
public:
FastqLoader();
void loadWithPeriod(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period);
int openWithPeriod(string file,int period);
int open(string file);
int getSize();
void load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator);
void close();
};
#endif
|
