Method printBAF

src/GenomeCopyNumber.cpp:1718–1739

}

void GenomeCopyNumber::printBAF(std::string const& outFile, SNPinGenome& snpingenome, std::string const& matefile) {
    string myName = outFile;
    string outfile = myName + "_BAF.txt";
	std::ofstream file (outfile.c_str());
	map<string,int>::iterator it;
	file << "Chromosome\tPosition\tBAF\tFittedA\tFittedB\tA\tB\tuncertainty";
	file << "\n";
	for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {

		string chrNumber = (*it).first;

        int indexSNP = snpingenome.findIndex(chrNumber);
        if (indexSNP == NA) {
		    cerr << "An error occurred in GenomeCopyNumber::printBAF: could not find an SNP index for "<<chrNumber<<"\n";
		    exit(-1);
        }
        printBAF(chrNumber,file,snpingenome.SNP_atChr(indexSNP), myName, matefile);


	}
	file.close();
}


void GenomeCopyNumber::deleteFlanks(int telo_centromeric_flanks) {