bedtools2/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h at 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb · arq5x/bedtools2 · GitHub

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/*
 * SingleLineTextFileReader.h
 *
 *  Created on: Nov 8, 2012
 *      Author: nek3d
 */

#ifndef SINGLELINETEXTFILEREADER_H_
#define SINGLELINETEXTFILEREADER_H_

#include <algorithm>
#include <stdint.h>
#include "FileReader.h"
#include "string.h"
#include "lineFileUtilities.h"

typedef int64_t CHRPOS;

class SingleLineDelimTextFileReader : public FileReader {
public:
	//Allow VCF records to access a specialized private method.
	//See end of class declaration for details.
	friend class VcfRecord;

	SingleLineDelimTextFileReader(int numFields, char delimChar = '\t');
	~SingleLineDelimTextFileReader();

	virtual bool readEntry();
	virtual int getNumFields() const { return _numFields; }
	virtual void getField(int numField, string &val) const;
	virtual void getField(int numField, CHRPOS &val) const; //this signaiture isn't const because it operates on an internal string for speed.
	virtual void getField(int fieldNum, char &val) const;
	virtual void appendField(int fieldNum, string &str) const;
	virtual const string &getHeader() const { return _header; }
	virtual bool hasHeader() const { return _fullHeaderFound; }
	virtual void setInHeader(bool val) { _inheader = val; }

protected:
	int _numFields;
	char _delimChar;
	string _header;
	bool _fullHeaderFound;
	int _currDataPos;
	string _sLine;
	int *_delimPositions;
	string _currChromStr;
	string _tempChrPosStr;
	int _lineNum;
	bool _inheader;
	bool detectAndHandleHeader();
	bool findDelimiters();

	//This is actually a very specialized function strictly for VCF
	//records to read and process extra information about Structural Variants.
	static const int VCF_TAG_FIELD = 7;
	CHRPOS getVcfSVlen();


};


#endif /* SINGLELINETEXTFILEREADER_H_ */