trimseqscommand.h

   1 #ifndef TRIMSEQSCOMMAND_H
   2 #define TRIMSEQSCOMMAND_H
   3
   4 /*
   5  *  trimseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 6/6/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "sequence.hpp"
  16
  17 class TrimSeqsCommand : public Command {
  18 public:
  19         TrimSeqsCommand(string);
  20         ~TrimSeqsCommand();
  21         int execute();
  22         void help();
  23
  24 private:
  25         void getOligos(vector<ofstream*>&);
  26         bool stripQualThreshold(Sequence&, ifstream&);
  27         bool cullQualAverage(Sequence&, ifstream&);
  28         bool stripBarcode(Sequence&, int&);
  29         bool stripForward(Sequence&);
  30         bool stripReverse(Sequence&);
  31         bool cullLength(Sequence&);
  32         bool cullHomoP(Sequence&);
  33         bool cullAmbigs(Sequence&);
  34         bool compareDNASeq(string, string);
  35
  36         bool abort;
  37         string fastaFile, oligoFile, qFileName, outputDir;
  38
  39         bool flip, allFiles, qtrim;
  40         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
  41         vector<string> forPrimer, revPrimer;
  42         map<string, int> barcodes;
  43         vector<string> groupVector;
  44 };
  45
  46 #endif