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#ifndef CHIMERABELLEROPHONCOMMAND_H
#define CHIMERABELLEROPHONCOMMAND_H
/*
* chimerabellerophoncommand.h
* Mothur
*
* Created by westcott on 4/1/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "mothurchimera.h"
/***********************************************************/
class ChimeraBellerophonCommand : public Command {
public:
ChimeraBellerophonCommand(string);
~ChimeraBellerophonCommand(){}
vector<string> setParameters();
string getCommandName() { return "chimera.bellerophon"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, filter, correction, removeChimeras;
string fastafile;
int processors, window, increment, numSeqs;
vector<string> outputNames;
};
/***********************************************************/
#endif
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