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/*
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 <http://www.gnu.org/licenses/>.
*/
/*
* Faster.hpp
*
* Created on: Feb 24, 2009
* Author: caa
*/
#ifndef FASTER_HPP_
#define FASTER_HPP_
#include <string>
#include <assert.h>
#include <iostream>
#include <stdint.h>
#include <vector>
#include <list>
#include <set>
#include <string>
#include <map>
#include <cmath>
#include "bam.h"
#include "Haplotype.hpp"
#include "Read.hpp"
#include "MLAlignment.hpp"
#include "ObservationModel.hpp"
using namespace std;
class ObservationModelS
{
protected:
class UngappedAlignment
{
public:
UngappedAlignment()
{
ll=-HUGE_VAL;
relPos=-10000;
numMismatch=10000;
}
UngappedAlignment(double _ll, int _relPos, int _numMismatch)
{
ll=_ll;
relPos=_relPos;
numMismatch=_numMismatch;
}
double ll;
int relPos;
int numMismatch;
};
public:
ObservationModelS() {};
ObservationModelS(const Haplotype & _hap, const Read & r, uint32_t hapStart, const ObservationModelParameters & _params);
virtual ~ObservationModelS();
MLAlignment align(const HapHash & hash);
//MLAlignment calcLikelihood();
//double getLogLikelihood() { calcLikelihood(); return ml.ll; };
// void changeHaplotype(const Haplotype & newHap);
void printAlignment(size_t hapScrPos);
void printStatistics();
ObservationModelParameters params;
protected:
void computeBMid();
void setupReadLikelihoods();
void Align();
void reportVariants();
inline void doTransition(int cs, int nr, const vector<int> & state, vector<double> & alpha, vector<double> & bt, const vector<double> & tr, const int & S);
inline void doTransitionNF(int cs, int nr, const vector<int> & state, vector<double> & alpha, vector<double> & bt, const vector<double> & tr, const int & S);
void SStateHMM(vector<int> & relPos);
void AlignHash(const HapHash & hash);
MLAlignment ml;
vector<double> logMatch, cumLogMatch, logMismatch;
vector<int> mapState;
double llMatch; //log likelihood when all bases in the read match
int bMid, hlen, rlen;
double llOff, llOffHMQ, pOffFirst, pOffFirstHMQ;
const Haplotype *hap_ptr;
const Read *read_ptr;
size_t hapStart;
bool likelihoodComputed, bMidError;
};
#endif /* FASTER_HPP_ */
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