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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "QualityCaller.h"
#include <RayPlatform/core/statistics.h>
#include <iostream>
#include <assert.h>
#include <math.h>
using namespace std;
/*
* \see http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
*/
double QualityCaller::computeCorrelation(vector<int>*x,vector<int>*y){
if(x->size()==0)
return 0;
#ifdef CONFIG_ASSERT
assert(x->size()==y->size());
#endif
double averageX=getAverage(x);
double averageY=getAverage(y);
double firstSum=0;
double deviationX=0;
double deviationY=0;
for(int i=0;i<(int)x->size();i++){
int xValue=x->at(i);
int yValue=y->at(i);
double diffX= xValue - averageX;
double diffY= yValue - averageY;
firstSum+= diffX * diffY;
deviationX+= diffX*diffX;
deviationY+= diffY*diffY;
}
if(deviationX==0 || deviationY==0)
return 0;
double correlation=(0.0+firstSum)/(sqrt(0.0+deviationX) * sqrt(0.0+deviationY));
return correlation;
}
double QualityCaller::computeQuality(map<CoverageDepth,LargeCount>*array1,map<CoverageDepth,LargeCount>*array2){
vector<int> y1Values;
vector<int> y2Values;
#ifdef CONFIG_CALLER_VERBOSE
cout<<"peakY for array1 "<<bestX<<endl;
#endif
for(map<CoverageDepth,LargeCount>::iterator i=array1->begin();i!=array1->end();i++){
int x1=i->first;
int y1=i->second;
/* array2 should alwayas have this point */
if(array2->count(x1) > 0){
int y2=(*array2)[x1];
#ifdef CONFIG_CALLER_VERBOSE_POINTS
cout<<"POINT "<<x1<<" "<<y1<<" "<<y2<<endl;
#endif
y1Values.push_back(y1);
y2Values.push_back(y2);
}
}
double correlation=computeCorrelation(&y1Values,&y2Values);
#ifdef CONFIG_CALLER_VERBOSE
cout<<"Correlation computed on "<<y1Values.size()<<" points."<<endl;
#endif
if(correlation<0)
correlation=-correlation;
/* the quality score is the absolute correlation coefficient */
return correlation;
}
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