qualityscores.h

   1 #ifndef QUALITYSCORES
   2 #define QUALITYSCORES
   3
   4 /*
   5  *  qualityscores.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 7/12/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "mothur.h"
  15 #include "mothurout.h"
  16 #include "sequence.hpp"
  17
  18 /**************************************************************************************************/
  19
  20 class QualityScores {
  21 public:
  22         QualityScores();
  23         QualityScores(ifstream&, int);
  24         string getName();
  25         void printQScores(ofstream&);
  26         void trimQScores(int, int);
  27         void flipQScores();
  28         bool stripQualThreshold(Sequence&, double);
  29         bool stripQualRollingAverage(Sequence&, double);
  30         bool stripQualWindowAverage(Sequence&, int, int, double);
  31         bool cullQualAverage(Sequence&, double);
  32 private:
  33
  34         double calculateAverage();
  35         MothurOut* m;
  36         vector<int> qScores;
  37
  38         string seqName;
  39         int seqLength;
  40 };
  41
  42 /**************************************************************************************************/
  43
  44 #endif