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#ifndef CHIMERAPERSEUSCOMMAND_H
#define CHIMERAPERSEUSCOMMAND_H
/*
* chimeraperseuscommand.h
* Mothur
*
* Created by westcott on 10/26/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "sequenceparser.h"
#include "sequencecountparser.h"
#include "myPerseus.h"
#include "counttable.h"
/***********************************************************/
class ChimeraPerseusCommand : public Command {
public:
ChimeraPerseusCommand(string);
~ChimeraPerseusCommand() = default;
vector<string> setParameters();
string getCommandName() { return "chimera.perseus"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.perseus\n"; }
string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, hasCount, dups, removeChimeras;
string fastafile, countfile;
int processors, alignLength;
double cutoff, alpha, beta;
vector<string> outputNames;
string getCountFile(string&);
vector<seqData> readFiles(string, map<string, int>);
int deconvoluteResults(string, string);
int createProcessesGroups(map<string, vector<string> >&, string, string, string, string, vector<string>, string, string, int&);
};
/***********************************************************/
#endif
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