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//
// filtersharedcommand.h
// Mothur
//
// Created by Sarah Westcott on 1/4/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_filtersharedcommand_h
#define Mothur_filtersharedcommand_h
#include "command.hpp"
#include "inputdata.h"
class FilterSharedCommand : public Command {
public:
FilterSharedCommand(string);
~FilterSharedCommand() = default;
vector<string> setParameters();
string getCommandName() { return "filter.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Filter.shared"; }
string getDescription() { return "remove OTUs based on various criteria"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, pickedGroups, allLines, makeRare, keepties;
set<string> labels; //holds labels to be used
string groups, label, sharedfile, accnosfile;
vector<string> Groups, outputNames;
int minAbund, minTotal, minSamples;
float minPercent, minPercentSamples, rarePercent;
int processShared(SharedRAbundVectors*&);
};
#endif
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