parsefastaqcommand.h

   1 #ifndef PARSEFASTAQCOMMAND_H
   2 #define PARSEFASTAQCOMMAND_H
   3
   4 /*
   5  *  parsefastaqcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/30/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class ParseFastaQCommand : public Command {
  17
  18 public:
  19         ParseFastaQCommand(string);
  20         ParseFastaQCommand();
  21         ~ParseFastaQCommand() {}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "parse.fastq";         }
  25         string getCommandCategory()             { return "Sequence Processing"; }
  26         string getOutputFileNameTag(string, string);
  27         string getHelpString();
  28         string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
  29         string getDescription()         { return "reads a fastq file and creates a fasta and quality file"; }
  30
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34 private:
  35
  36         vector<string> outputNames;
  37         string outputDir, fastaQFile;
  38         bool abort, fasta, qual;
  39
  40         vector<int> convertQual(string);
  41 };
  42
  43 #endif
  44
  45