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);
24 vector<string> setParameters();
25 string getCommandName() { return "make.fastq"; }
26 string getCommandCategory() { return "Sequence Processing"; }
27 string getHelpString();
28 string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
31 void help() { m->mothurOut(getHelpString()); }
36 string fastafile, qualfile, outputDir;
38 vector<string> outputNames;
40 string convertQual(vector<int>);