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//
// mergecountcommand.hpp
// Mothur
//
// Created by Sarah Westcott on 8/3/16.
// Copyright © 2016 Schloss Lab. All rights reserved.
//
#ifndef mergecountcommand_hpp
#define mergecountcommand_hpp
#include "command.hpp"
class MergeCountCommand : public Command {
#ifdef UNIT_TEST
//friend class TestMergeCountCommand;
#endif
public:
MergeCountCommand(string);
~MergeCountCommand() = default;
vector<string> setParameters();
string getCommandName() { return "merge.count"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Merge.count"; }
string getDescription() { return "reads count files and combines them into a single count file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string inputDir, countfile, output, outputFileName;
vector<string> outputNames, fileNames;
int numInputFiles;
};
#endif /* mergecountcommand_hpp */
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