1 #ifndef MAKEFASTQCOMMAND_H
2 #define MAKEFASTQCOMMAND_H
8 * Created by westcott on 2/14/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
16 class MakeFastQCommand : public Command {
20 MakeFastQCommand(string);
23 vector<string> getRequiredParameters();
24 vector<string> getValidParameters();
25 vector<string> getRequiredFiles();
26 map<string, vector<string> > getOutputFiles() { return outputTypes; }
32 string fastafile, qualfile, outputDir;
34 vector<string> outputNames;
35 map<string, vector<string> > outputTypes;
37 string convertQual(vector<int>);