Method focusOnCapture

src/GenomeCopyNumber.cpp:4199–4293

	return numberOfRemovedExons/totalNumberExons;
}
int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) {
	ifstream file (captureFile.c_str());
	string line;
    //string::size_type pos = 0;
    string currentChr = "";
    int index = NA;
    int count = 0;
    int mapCount;
    float ratio;
    int endShift = - windowSize_/step_ + 1;
    unsigned long int minRegion = refGenomeSize_;
    refGenomeSize_=0; //will be recalculated!!!

    map<int,int> chrRead;
    map<int,int>::iterator itMapChr;

    int averageReadLength=400; averageReadLength=150;//from version 6.6

	if (file.is_open())	{
	    cout << "..Reading "<< captureFile << "\n";
        cout << "..Your file must be in .BED format, and it must be sorted\n";

		while (! file.eof() )	{
			getline (file,line);
			if (! line.length()) continue;
            std::vector<std::string> strs = split(line, '\t');
            if (strs.size()<3) continue;

			string chr = strs[0];
            processChrName(chr);
            int positionS = atoi(strs[1].c_str())-averageReadLength; if (positionS<=0) positionS=1;
            int positionE = atoi(strs[2].c_str())-1; //because it is 1-based

            if (positionS >= positionE || positionS<0) continue;

			if ( currentChr.compare(chr)!=0 ){ //start reading a new chromosome
                cout << "..Reading capture for chromosome " << chr << "\n";
                index = findIndex(chr);
                if (index == NA) {
				    cout <<  "skipping chromosome " << chr << "\n";
				    continue;
                }
                //restore all variables for a new chromosome
                currentChr = chr;
                //check if the file is sorted:
                itMapChr=chrRead.find(index);
                if (itMapChr != chrRead.end()  ) {
                    cerr << "Your .bed file should be sorted. \n..Unable to proceed..\n";
                    exit(-1);
                }
                chrRead[index]=1;

                //check is notNprofile_ exists, and create it if it does not exists:
                chrCopyNumber_[index].checkOrCreateNotNprofileWithZeros();
                //cout <<  "..Index for chromosome " << currentChr << ": "<< index << "\n";
			}
            count ++;