| base_trans | DNPclass | [private] |
| cand_bases | DNPclass | [private] |
| cand_vec | DNPclass | [private] |
| column_is_candidate(int col) | DNPclass | [private] |
| confirmed_DNP_pos | DNPclass | [private] |
| cons_bases | DNPclass | [private] |
| Dmin | DNPclass | [private] |
| DNPclass(MAl_addon *mal, int minqual, int d_min=3, double p_max=0.001) | DNPclass | |
| evaluate_DNP_candidate_positions() | DNPclass | [private] |
| find_DNP_base_candidates(int &a, int &t, int &c, int &g, int &gap, char seqbase, int &tot_seqbase, int &tot_others) | DNPclass | [private] |
| find_DNP_candidate_positions() | DNPclass | [private] |
| look_for_corr(vector< char > &first_col, vector< char > &second_col, vector< int > &first_qual_col, vector< int > &second_qual_col, char cand_base_1, char cand_base_2, int &num_err_first, int &num_err_second, double &exp_err_first, double &exp_err_second, int &num_corr, double &expectation_val) | DNPclass | [private] |
| m | DNPclass | [private] |
| num_candidates | DNPclass | [private] |
| num_found | DNPclass | [private] |
| num_pos | DNPclass | [private] |
| p_tot_max | DNPclass | [private] |
| pick_base_row_and_qual_columns(int firstDNPindex, int secondDNPindex, vector< char > &firstDNPvec, vector< char > &secondDNPvec, vector< int > &first_qual_vec, vector< int > &second_qual_vec, vector< int > &rownum_vec) | DNPclass | [private] |
| poisson_probability(double lambda, int obs) | DNPclass | [private] |
| quality2error | DNPclass | [private] |
| qualmin | DNPclass | [private] |
| set_DNPs(int col1, int col2, char DNPbase1, char DNPbase2, vector< int > &rownum_vec, int ID1, int ID2, char cons1, char cons2) | DNPclass | [private] |
| ~DNPclass() | DNPclass | |
