makefastqcommand.h

   1 #ifndef MAKEFASTQCOMMAND_H
   2 #define MAKEFASTQCOMMAND_H
   3
   4 /*
   5  *  makefastqcommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 2/14/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class MakeFastQCommand : public Command {
  17
  18 public:
  19
  20         MakeFastQCommand(string);
  21         MakeFastQCommand();
  22         ~MakeFastQCommand(){}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "make.fastq";                          }
  26         string getCommandCategory()             { return "Sequence Processing";         }
  27         string getOutputFileNameTag(string, string);
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
  30         string getDescription()         { return "creates a fastq file from a fasta and quality file"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38
  39         string fastafile, qualfile, outputDir;
  40         bool abort;
  41         vector<string> outputNames;
  42
  43         string convertQual(vector<int>);
  44
  45 };
  46
  47 #endif
  48
  49