parsesffcommand.h

   1 #ifndef PARSESFFCOMMAND_H
   2 #define PARSESFFCOMMAND_H
   3
   4 /*
   5  *  parsesffcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 2/6/10.
   9  *  Copyright 2010 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class ParseSFFCommand : public Command {
  17 public:
  18         ParseSFFCommand(string);
  19         ParseSFFCommand();
  20         ~ParseSFFCommand();
  21         vector<string> getRequiredParameters();
  22         vector<string> getValidParameters();
  23         vector<string> getRequiredFiles();
  24         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  25         int execute();
  26         void help();
  27
  28 private:
  29
  30         int parseHeaderLineToInt(ifstream&);
  31         vector<float> parseHeaderLineToFloatVector(ifstream&, int);
  32         vector<int> parseHeaderLineToIntVector(ifstream&, int);
  33         string parseHeaderLineToString(ifstream&);
  34         void screenFlow(vector<float>, int&);
  35         string flow2seq(vector<float>, int);
  36         bool screenSeq(string&, int&);
  37         bool compareDNASeq(string, string);
  38         void getOligos(vector<ofstream*>&);
  39
  40
  41         string sffFile;
  42         string oligoFile;
  43
  44         int minLength;
  45         int numFPrimers, numRPrimers, numBarcodes;
  46         vector<string> forPrimer, revPrimer;
  47         map<string, int> barcodes;
  48         vector<string> groupVector;
  49         vector<string> outputNames;
  50         map<string, vector<string> > outputTypes;
  51
  52 //      string stripSeqQual(string, int, int);
  53 //      string stripQualQual(string, int, int);
  54
  55         string outputDir;
  56         bool abort;
  57 };
  58
  59 #endif
  60
  61