Method processReadWithBowtie

src/GenomeCopyNumber.cpp:4131–4178

}

int GenomeCopyNumber::processReadWithBowtie(std::string const& inputFormat, std::string const& matesOrientation,std::string const line,std::string const line2) {

    int valueToReturn = 0;

    string chr1, chr2, orient1, orient2;

	if ((inputFormat.compare("bowtie")==0 || inputFormat.compare("Bowtie")==0)&&(matesOrientation.compare("0")!=0)){

			if (! line2.length()) return 0;
			std::vector<std::string> strs = split(line, '\t');
			std::vector<std::string> strs2 = split(line2, '\t');
			if ((strs.size() > 4)&&(strs2.size() > 4)) {
				string chr1 = strs[2];
				string chr2 = strs2[2];

				processChrName(chr1);
				processChrName(chr2);
				if (chr1.compare(chr2)==0) {

                    string orient1 = strs[1];
                    string orient2 = strs2[1];
                    if (orient1.compare("+")==0)
                        orient1 = "F";
                    else
                        orient1 = "R";

                    if (orient2.compare("+")==0)
                        orient2 = "F";
                    else
                        orient2 = "R";
                    int left = atoi(strs[3].c_str());
                    int right = atoi(strs2[3].c_str());

                    if ((matesOrientation.compare(orient1+orient2)==0 && (right-left>0)) || (matesOrientation.compare(orient2+orient1)==0 && (right-left<0))) {
                        int index = findIndex(chr1);
                        if (index!=NA) {
                            chrCopyNumber_[index].mappedPlusOneAtI(min(left,right),step_);
                            valueToReturn=1;
                        }
                    }
                }
			}
			strs.clear();
			strs2.clear();
            return valueToReturn;
	}
	return 0;
}
float GenomeCopyNumber::removeLargeExons(float iqrToKeep) {
    float maxLength = 0;
	vector<ChrCopyNumber>::iterator it;