src/mismatchmodel.h

#ifndef MISMATCH_H
#define MISMATCH_H

#include "frequencymatrix.h"

class FragHit;
class Target;

class MismatchTable {
  std::vector<FrequencyMatrix<double> > _first_read_mm;
  std::vector<FrequencyMatrix<double> > _second_read_mm;
  FrequencyMatrix<double> _insert_params;
  FrequencyMatrix<double> _delete_params;
  size_t _max_len;
  bool _active;

 public:
  MismatchTable(double alpha);
  MismatchTable(std::string param_file_name);
  void activate(bool active = true) { _active = active; }
  void get_indices(const FragHit& f,
                   std::vector<char>& left_indices,
                   std::vector<char>& left_seq,
                   std::vector<char>& left_ref,
                   std::vector<char>& right_indices,
                   std::vector<char>& right_seq,
                   std::vector<char>& right_ref) const;
  double log_likelihood(const FragHit& f) const;
  void update(const FragHit&, double p, double mass);
  void fix();
  void append_output(std::ofstream& outfile) const;
};

#endif