Method intersectWithBedtools

src/BAFpileup.cpp:245–292

}

std::string BAFpileup::intersectWithBedtools(std::string makeminipileup, std::string outputDir, std::string bedFileWithRegionsOfInterest, std::string chrLen)
{
    FILE *stream;
    std::string intersected = outputDir + "_SNPinNewCaptureRegions.bed";

    if (makeminipileup.substr(makeminipileup.size()-3,3).compare("vcf")==0 || makeminipileup.substr(makeminipileup.size()-6,6).compare("vcf.gz")==0) {
        intersected = outputDir + "_SNPinNewCaptureRegions.vcf";
    }

    string command = pathToBedtools_ +" intersect -a " + makeminipileup + " -b " + bedFileWithRegionsOfInterest + " > " + intersected;

    stream =
    #if defined(_WIN32)
        _popen(command.c_str(), "w");
    #else
        popen(command.c_str(), "w");
    #endif

    #if defined(_WIN32)
    _pclose(stream);
    #else
    pclose(stream);
    #endif

    remove(bedFileWithRegionsOfInterest.c_str());

    if (makeminipileup.substr(makeminipileup.size()-3,3).compare("bed")==0) {
        return intersected;
    }

    //else: VCF input format; need to transform into BED
    ifstream file (intersected.c_str());
    ofstream myfile;
    std::string intersectedBed = outputDir + "_SNPinNewCaptureRegions.bed";
    myfile.open(intersectedBed.c_str());
    std:: string line;
    int nb_snp = 0;
    while (std::getline(file,line))  {
        nb_snp++;
        std::vector<std::string> strs = split(line, '\t');
        myfile << strs[0] << "\t"<< atoi(strs[1].c_str()) -1 << "\t" <<  atoi(strs[1].c_str()) << "\t" << strs[3] << "\t" << strs[4]<<"\n";
    }
    cout << "..will use "<<nb_snp<<" SNPs for calculation of the BAF profile\n";
    myfile.close();
    file.close();
    remove(intersected.c_str());
    return intersectedBed;
}

std::string BAFpileup::createPileUpFile(std::string outputDir, std::string samtools_path, std::string pathToSambamba,std::string SambambaThreads , std::string control_MateFile, std::string intersected, std::string fastaFile, int minQualPerPos)
{