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/*
Ray
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 _Read
#define _Read
#include <code/SequencesIndexer/PairedRead.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <string>
#include <stdint.h>
#include <vector>
#include <fstream>
using namespace std;
#define TYPE_SINGLE_END 0
#define TYPE_LEFT_END 1
#define TYPE_RIGHT_END 2
/**
* a read is represented as a uint8_t*,
* 2 bits per nucleotide
* and a (possible) link to paired information.
* \author Sébastien Boisvert
*/
class Read{
PairedRead m_pairedRead;// the read on the left
uint8_t *m_sequence;
/* maximum value: 65535 */
uint16_t m_length;
uint8_t m_type;
// for the scaffolder:
uint8_t m_forwardOffset;
uint8_t m_reverseOffset;
char*trim(char*a,const char*b);
public:
void constructor(const char*sequence,MyAllocator*seqMyAllocator,bool trim);
void constructorWithRawSequence(const char*sequence,uint8_t*raw,bool trim);
void getSeq(char*buffer,bool color,bool doubleEncoding)const;
int length()const;
Kmer getVertex(int pos,int w,char strand,bool color)const;
bool hasPairedRead()const;
PairedRead*getPairedRead();
uint8_t*getRawSequence();
int getRequiredBytes();
void setRawSequence(uint8_t*seq,int length);
void setRightType();
void setLeftType();
int getType();
void setType(uint8_t type);
void setForwardOffset(int a);
void setReverseOffset(int a);
int getForwardOffset();
int getReverseOffset();
void writeOffsets(ostream*f);
void readOffsets(istream*f);
void write(ostream*f);
void read(istream*f,MyAllocator*seqMyAllocator);
} ATTRIBUTE_PACKED;
#endif
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