1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
/*
* Singleerrorrate.h
*
* Created on: Jan 23, 2015
* Author: Quentin Marcou
*
* This source code is distributed as part of the IGoR software.
* IGoR (Inference and Generation of Repertoires) is a versatile software to analyze and model immune receptors
* generation, selection, mutation and all other processes.
* Copyright (C) 2017 Quentin Marcou
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
#ifndef SINGLEERRORRATE_H_
#define SINGLEERRORRATE_H_
#include "Errorrate.h"
#include "Utils.h"
#include <math.h>
//Debug
#include <iostream>
/**
* \class Single_error_rate Singleerrorrate.h
* \brief Independent single nucleotide error model.
* \author Q.Marcou
* \version 1.0
*
* Simplest instance of the ErrorRate family. Models errors/mutations as a Bernouilli process with a global rate independent of position and context.
*/
class Single_error_rate: public Error_rate {
public:
Single_error_rate();
Single_error_rate(double);
virtual ~Single_error_rate();
double compare_sequences_error_prob( double ,const std::string& , Seq_type_str_p_map& , const Seq_offsets_map& , const std::unordered_map<std::tuple<Event_type,Gene_class,Seq_side>, std::shared_ptr<Rec_Event>>& , Mismatch_vectors_map& , double& , double& );
void update();
void add_to_norm_counter();
void clean_seq_counters();
Single_error_rate operator+(Single_error_rate);
Single_error_rate& operator+=(Single_error_rate);
void write2txt(std::ofstream&);
std::shared_ptr<Error_rate> copy()const;
std::string type() const {return "SingleErrorRate";}
Error_rate* add_checked (Error_rate*);
const double& get_err_rate_upper_bound(size_t,size_t) ;
void build_upper_bound_matrix(size_t,size_t);
int get_number_non_zero_likelihood_seqs() const{return number_seq;};
std::queue<int> generate_errors(std::string& , std::mt19937_64&) const;
private:
double model_rate;
double normalized_counter;
long double seq_weighted_er;
int number_errors;
int genomic_nucl;
long double temp2;
long double temp;
int subseq_compare_err_num(const std::string& , const std::string&);
//TODO use seq likelihood to extract the likelihood of the model on the fly
};
#endif /* SINGLEERRORRATE_H_ */
|
