Method calculateVarianceForNormalCopy

src/GenomeCopyNumber.cpp:3343–3375

float GenomeCopyNumber::calculateVarianceForNormalCopy(int ploidy) { //geting the total variance for points with median around 1 (+-0.5/ploidy) ---  OLD
	float variance = 0;
	int count = 0;
	double lowBoundary = 1-0.5/ploidy;
	double highBoundary = 1+0.5/ploidy;
	float value,med;
	vector<ChrCopyNumber>::iterator it;

	ofstream myfile;

	myfile.open ("example.txt");


	cout << "..Calculating variance for neutral copies\n";
	for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
		//cout << "..processing chromosome " <<it->getChromosome()<<"\n";
		for (int i = 0; i<it->getLength(); i++) {
			med = it->getMedianProfileAtI(i);
			if ((med>lowBoundary)&&(med < highBoundary)) {
				value = it->getRatioAtBin(i);
				if (isRatioLogged_&& value!=NA)
                    value=pow(2,value);
				if (value != NA) {
					myfile << value-1 << "\n";
					variance += (value-1)*(value-1);
					count++;
				}
			}
		}
	}
	myfile.close();
	return float(variance/(count-1));
}

void GenomeCopyNumber::printPloidy(std::string const& outFile) {
	std::ofstream file (outFile.c_str());