Method readGemMappabilityFile

src/GenomeCopyNumber.cpp:2500–2640

}

void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) {
	ifstream file (inFile.c_str());
	string line;
    string::size_type pos = 0;
    string currentChr = "";
    int index = NA;
    int count = 0;
    int uniqueCount = 0;
    int localWindowSize = windowSize_;
    float ratio;
    int positionInd = 0;
    int startPos = 0;
    int endPos = 0;
    int lastEnd = -1;
    string text = "";
	if (file.is_open())	{
	    cout << "..Reading "<< inFile << "\n";
	    int countChromosomes = 0;
	    int countChromosomesOutOfIndex = 0;
	    isMappUsed_=true;
		while (! file.eof() )	{
			getline (file,line);
			if (! line.length()) continue;
			pos = 0;
			if ( (line.substr(0,1) == "~") && (line.substr(0,2) != "~~")){
			//if ( ( pos = line.find("~chr", pos)) != string::npos ){
                //save the last info:
                if (count > endPos && index != NA) { // endPos ?
                    int howMuchToDelete = startPos-lastEnd-1;
                    text = text.substr(howMuchToDelete);
                    uniqueCount =0;
                    for(int i = 0; i < (int)text.length(); ++i)
                        if (text[i] == '!')
                            uniqueCount++;

                    ratio = float(uniqueCount)/localWindowSize;
                    chrCopyNumber_[index].setMappabilityProfileAt(positionInd, ratio);
                }
                //restore all variables for a new chromosome
                if ( ( pos = line.find("~chr", pos)) != string::npos ){
                    currentChr = line.substr(4);
                } else {
                    currentChr = line.substr(1);
                }
                cout << "..Reading mappability for chromosome " << currentChr << "\n";
                index = findIndex(currentChr);

                positionInd = 0;
				count = 0;
				uniqueCount = 0;
                text = "";
                lastEnd = -1;

                //cout <<  "..Index for chromosome " << currentChr << ": "<< index << "\n";

				if (index == NA) {
				    cout <<  "skipping chromosome " << currentChr << "\n";
				    countChromosomesOutOfIndex ++;