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&);
  24         string getName();
  25
  26         vector<int> getQualityScores() { return qScores; }
  27         void printQScores(ofstream&);
  28         void trimQScores(int, int);
  29         void flipQScores();
  30         bool stripQualThreshold(Sequence&, double);
  31         bool stripQualRollingAverage(Sequence&, double);
  32         bool stripQualWindowAverage(Sequence&, int, int, double);
  33         bool cullQualAverage(Sequence&, double);
  34         void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
  35         void updateForwardMap(vector<vector<int> >&, int, int, int);
  36         void updateReverseMap(vector<vector<int> >&, int, int, int);
  37
  38 private:
  39
  40         double calculateAverage();
  41         MothurOut* m;
  42         vector<int> qScores;
  43
  44         string seqName;
  45         int seqLength;
  46 };
  47
  48 /**************************************************************************************************/
  49
  50 #endif