1 #ifndef SUMMARYQUALCOMMAND_H
2 #define SUMMARYQUALCOMMAND_H
3 
4 /*
5  *  summaryqualcommand.h
6  *  Mothur
7  *
8  *  Created by westcott on 11/28/11.
9  *  Copyright 2011 Schloss Lab. All rights reserved.
10  *
11  */
12 
13 
14 #include "command.hpp"
15 #include "qualityscores.h"
16 
17 /**************************************************************************************************/
18 
19 class SummaryQualCommand : public Command {
20 public:
21 	SummaryQualCommand(string);
22 
~SummaryQualCommand()23 	~SummaryQualCommand(){}
24 
25 	vector<string> setParameters();
getCommandName()26 	string getCommandName()			{ return "summary.qual";			}
getCommandCategory()27 	string getCommandCategory()		{ return "Sequence Processing";		}
28 
29 	string getHelpString();
30     string getOutputPattern(string);
getCitation()31 	string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
getDescription()32 	string getDescription()		{ return "summarize the quality of a set of sequences"; }
33 
34 	int execute();
help()35 	void help() { m->mothurOut(getHelpString()); }
36 
37 private:
38 	bool abort, hasNameMap;
39 	string qualfile,  namefile, countfile;
40 	vector<string> outputNames;
41 	map<string, int> nameMap;
42 	int processors;
43 
44 	long long createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string);
45 	int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
46 };
47 /**************************************************************************************************/
48 
49 #endif
50 
51