1 #ifndef PARSEFASTAQCOMMAND_H
2 #define PARSEFASTAQCOMMAND_H
8 * Created by westcott on 9/30/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
16 class ParseFastaQCommand : public Command {
19 ParseFastaQCommand(string);
21 ~ParseFastaQCommand();
22 vector<string> getRequiredParameters();
23 vector<string> getValidParameters();
24 vector<string> getRequiredFiles();
25 map<string, vector<string> > getOutputFiles() { return outputTypes; }
31 vector<string> outputNames;
32 map<string, vector<string> > outputTypes;
33 string outputDir, fastaQFile;
36 vector<int> convertQual(string);