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
  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"; }
  32
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37
  38 private:
  39
  40         string fastafile, qualfile, outputDir, format;
  41         bool abort;
  42         vector<string> outputNames;
  43
  44         string convertQual(vector<int>);
  45
  46 };
  47
  48 #endif
  49
  50