Method createPileUpFile

src/BAFpileup.cpp:294–321

}

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)
{
    string minipileup = outputDir + "_minipileup" +".pileup";
    FILE *stream;

    string command;
    if (pathToSambamba != "")    {
        string samtools_arg = "--samtools -f " +fastaFile+ " -d 8000 -Q "+int2string(minQualPerPos)+ " -q 1 -l " + intersected;
        command  = pathToSambamba + " mpileup -t " + SambambaThreads + " -o " + minipileup + " " + control_MateFile + " " + samtools_arg ;
    }  else   {
         command = samtools_path + " mpileup -f "+fastaFile+" -d 8000 -Q "+int2string(minQualPerPos)+" -q 1 -l " + intersected + " " + control_MateFile + " > " + minipileup; //discard reads wit 0 mapping quality
    }

    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
    cout << "..If you have got an error at this step and a mini-pileup file is empty, check that you are using samtools v1.1 or later and provide a corresponding path in your config file"<<endl;
    return minipileup;
}

/*
std::vector < std::vector<float> >BAFpileup::computeBAF(GenomeCopyNumber & sampleorcontrol, std::string minipileup, std::string outputDir,  std::string filename)