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#ifndef MAKEFASTQCOMMAND_H
#define MAKEFASTQCOMMAND_H
/*
* makefastqcommand.h
* mothur
*
* Created by westcott on 2/14/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
class MakeFastQCommand : public Command {
public:
MakeFastQCommand(string);
~MakeFastQCommand(){}
vector<string> setParameters();
string getCommandName() { return "make.fastq"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
string getDescription() { return "creates a fastq file from a fasta and quality file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string fastafile, qualfile, format;
bool abort;
vector<string> outputNames;
string convertQual(vector<int>);
};
#endif
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