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         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31
  32         string fastafile, qualfile, outputDir;
  33         bool abort;
  34         vector<string> outputNames;
  35         map<string, vector<string> > outputTypes;
  36
  37         string convertQual(vector<int>);
  38
  39 };
  40
  41 #endif
  42
  43