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"; }
28 string getHelpString();
29 string getOutputPattern(string);
30 string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
31 string getDescription() { return "creates a fastq file from a fasta and quality file"; }
35 void help() { m->mothurOut(getHelpString()); }
40 string fastafile, qualfile, outputDir, format;
42 vector<string> outputNames;
44 string convertQual(vector<int>);