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//
// getmimarkspackagecommand.h
// Mothur
//
// Created by Sarah Westcott on 3/25/14.
// Copyright (c) 2014 Schloss Lab. All rights reserved.
//
#ifndef Mothur_getmimarkspackagecommand_h
#define Mothur_getmimarkspackagecommand_h
#include "command.hpp"
#include "oligos.h"
#include "filefile.hpp"
/**************************************************************************************************/
class GetMIMarksPackageCommand : public Command {
public:
GetMIMarksPackageCommand(string);
~GetMIMarksPackageCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.mimarkspackage"; }
string getCommandCategory() { return "Sequence Processing"; }
string getOutputPattern(string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/get.mimarkspackage"; }
string getDescription() { return "create blank mimarks package form for sra command"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, requiredonly, setOligosParameter;
string oligosfile, groupfile, package, inputfile, file, inputDir;
vector<string> outputNames;
set<string> Groups;
void createGroupNames(Oligos& oligos);
int readFile();
};
/**************************************************************************************************/
#endif
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