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#ifndef REMOVERARECOMMAND_H
#define REMOVERARECOMMAND_H
/*
* removerarecommand.h
* mothur
*
* Created by westcott on 1/21/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "listvector.hpp"
#include "sharedrabundvectors.hpp"
class RemoveRareCommand : public Command {
public:
RemoveRareCommand(string);
~RemoveRareCommand(){}
vector<string> setParameters();
string getCommandName() { return "remove.rare"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, groups, label;
int nseqs, allLines;
bool abort, byGroup;
vector<string> outputNames, Groups;
set<string> labels;
void processSabund();
void processRabund();
int processList();
void processShared();
void processLookup(SharedRAbundVectors*&);
};
#endif
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