trash.h

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#ifndef TRAPPERTRASH_H
#define TRAPPERTRASH_H

#include "RW_algo.h"

#include <vector>

class TrashAlgo : public RWAlgo
{
public:
  TrashAlgo(TrapperDoc * pDoc_, std::set< db_recno_t >& recnoList, AlgoParam* param) : 
    RWAlgo(pDoc_, recnoList, param) {}
  
  void start();
  
  void trash(size_t seqNumber);
  
  int check_qual_in_win(int start, int stop, int ID, int &curr_win_good);
  void kill_read( int ID );
  
private:
  vector<double> logQual_to_quality;
  vector<double> decode_qualval_square;
  int TRASH_WINDOW_LEN;
  int TRASH_WINDOW_STEP;
  int MIN_NUM_ADJ_WIN_GOOD;
  int MIN_LEN_GOOD;
  double GOOD_PERCENTAGE;
  double MAX_VARIANCE_IN_QUALWIN;


};


#endif //TRAPPERTRASH_H

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