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/*
* 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 _FastqGzLoader
#define _FastqGzLoader
#ifdef CONFIG_HAVE_LIBZ
#include "LoaderInterface.h"
#include "Read.h"
#include "ArrayOfReads.h"
#include <RayPlatform/memory/MyAllocator.h>
#include <zlib.h>
#include <string>
#include <vector>
using namespace std;
/**
* This class is responsible for reading .fastq.gz files.
* \author Sébastien Boisvert
*/
class FastqGzLoader: public LoaderInterface{
bool m_completed;
bool m_noMoreBytes;
bool m_debug;
/* stuff for readahead */
int m_bufferedBytes;
int m_currentStart;
int m_firstNewLine;
char*m_readaheadBuffer;
gzFile m_f;
int m_size;
int m_loaded;
bool readOneSingleLine(char*buffer,int maximumLength);
bool pullLineWithReadaheadTechnology(char*buffer,int maximumLength);
public:
FastqGzLoader();
int openWithPeriod(string file,int period);
void loadWithPeriod(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period);
int open(string file);
int getSize();
void load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator);
void close();
};
#endif
#endif
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