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#ifndef SHHHSEQSCOMMAND_H
#define SHHHSEQSCOMMAND_H
/*
* shhhseqscommand.h
* Mothur
*
* Created by westcott on 11/8/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "myseqdist.h"
#include "seqnoise.h"
#include "sequenceparser.h"
#include "uniqueseqscommand.h"
#include "clustercommand.h"
//**********************************************************************************************************************
class ShhhSeqsCommand : public Command {
public:
ShhhSeqsCommand(string);
~ShhhSeqsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "shhh.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
string getDescription() { return "shhh.seqs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string fastafile, namefile, groupfile;
int processors;
double sigma;
vector<string> outputNames;
int readData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&);
vector<string> createProcessesGroups(string, string, string);
int deconvoluteResults(string, string);
};
/**************************************************************************************************/
#endif
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