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#pragma once
#ifndef CPAIRED_READ_SET_H_
#define CPAIRED_READ_SET_H_
#include "FileOutputBuffer.h"
#include "ReadsFileParser.h"
#include "ReadInBitsSet.h"
#include "ReadInBits.h"
#include "ColorSpaceRead.h"
#include "ShortReadUtil.h"
#include "MismatchScores.h"
#include "ReadsQualScores.h"
#include <vector>
#include <iostream>
#include <string>
using namespace std;
class CPairedReadsSet
{
public:
CPairedReadsSet(void);
CPairedReadsSet(unsigned int Capacity, unsigned int uiReadLength);
// Generate set given a file with reads and readLength (must be known in advance)
CPairedReadsSet(const char* InputFile, const char* fileFormat,\
unsigned int uiReadLength, bool in5to3cat3to5Format, unsigned int allowedNumOfNinRead, unsigned int readStartIndex = 0);
virtual ~CPairedReadsSet();
void ignoreQScores(void);
// unsigned int get_next_capacity_reads_pairs_from_single_file(void);
CReadInBitsSet* F_Reads;
CReadInBitsSet* R_Reads;
unsigned int allowedNumOfNinRead;
unsigned int uiRead_Length;
unsigned int uiNo_of_Reads;
unsigned int uiNo_of_Bad_Reads;
bool in5to3cat3to5Format;
// A char flag used to record the input file type, example F for fasta, S for .seq.txt, A for .realign
char cFileType;
char InputFile[FILENAME_MAX];
// Keep the info of the quality score
CReadsQualScores* pQualScoresF;
CReadsQualScores* pQualScoresR;
protected:
// get reads from the file and store (append) in a vector. Return how many reads are read-in.
unsigned int openAFileReady2GetRead(const char* InputFile, const char* fileFormat, unsigned int uiExpReadsStrLength, bool bDiscardReadsWN = false);
void save_next_read_id(const char* tagLine, char sep = ',');
CReadsFileParser parser;
void clearReads(void);
void removeExtraTags(void);
void getQualityScoresFromQUAL(void);
void handleBadRead(void);
unsigned int getExpReadLength(unsigned int getExpReadLength);
private:
int initialization(void);
};
#endif
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