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#ifndef SUMMARYQUALCOMMAND_H
#define SUMMARYQUALCOMMAND_H
/*
* summaryqualcommand.h
* Mothur
*
* Created by westcott on 11/28/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "qualityscores.h"
/**************************************************************************************************/
class SummaryQualCommand : public Command {
public:
SummaryQualCommand(string);
~SummaryQualCommand(){}
vector<string> setParameters();
string getCommandName() { return "summary.qual"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
string getDescription() { return "summarize the quality of a set of sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, hasNameMap;
string qualfile, namefile, countfile;
vector<string> outputNames;
map<string, int> nameMap;
int processors;
long long createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string);
int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
};
/**************************************************************************************************/
#endif
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