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() {}
23 vector<string> setParameters();
24 string getCommandName() { return "fastq.info"; }
25 string getCommandCategory() { return "Sequence Processing"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
30 string getDescription() { return "reads a fastq file and creates a fasta and quality file"; }
34 void help() { m->mothurOut(getHelpString()); }
37 vector<string> outputNames;
38 string outputDir, fastaQFile, format;
39 bool abort, fasta, qual, pacbio;
41 vector<int> convertQual(string);
42 vector<char> convertTable;