Method fillMyHash

src/GenomeCopyNumber.cpp:270–418

}

void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string const& inputFormat_str, std::string const& matesOrientation_str, int windowSize , int step, std::string targetBed) {
	//read mateFileName and calculate copyNumber
	long count = 0;
	long normalCount = 0;
	int bin = 0;

	cout << "..[genomecopynumber] Starting reading "<< mateFileName << "\n";
	//if (mateFileName.substr(mateFileName.size()-1,3).compare(".gz")==0) {
	//	igzstream in( mateFileName );
	//	if ( ! in.good()) {
	//		std::cerr << "ERROR: Opening file `" << mateFileName << "' failed.\n";
	//		return EXIT_FAILURE;
	//	}
	//	in.close();
	//}
	std::ifstream fileMates (mateFileName.c_str());
	vector<float> insertSizeVector;
	windowSize_ = windowSize;
	step_=step;
	string line;
	if (!fileMates.is_open()) {
	    cerr << "Error: unable to open "+mateFileName+"\n" ;
	    exit(-1);
	}

#ifdef PROFILE_TRACE
	time_t t0 = time(NULL);
#endif

	MateOrientation matesOrientation = getMateOrientation(matesOrientation_str);

	InputFormat inputFormat;
	char* line_buffer;
    if (inputFormat_str.compare("bam")==0 || inputFormat_str.compare("BAM")==0 || mateFileName.substr(mateFileName.size()-4,4).compare(".bam")==0 || mateFileName.substr(mateFileName.size()-3,3).compare(".gz")==0) {

        fileMates.close();

        FILE *stream;
        char buffer[MAX_BUFFER];
        string command;

        string myInputFormat=inputFormat_str;
        if (mateFileName.substr(mateFileName.size()-3,3).compare(".gz")!=0) {
	  if (mateFileName.substr(mateFileName.size()-4,4).compare(".bam")==0) {
                if (pathToSambamba_ != "")
                    {
                    command = pathToSambamba_ + " view -t " + SambambaThreads_ + " " + mateFileName;
                    myInputFormat="sam";       //will try to use existing sambamba
                    //cout << "..sambamba should be installed to be able to read BAM files; will use the following command for sambamba: "<<pathToSambamba_ + " view -t " + SambambaThreads_ + " " + mateFileName << "\n";
                    cout << "..sambamba should be installed to be able to read BAM files; will use the following command for sambamba: "<< command << "\n";
                    }
                else
                    {
		    command = pathToSamtools_ + " view -@ " + SambambaThreads_ + " " +mateFileName;
                    myInputFormat="sam";       //will try to use existing samtools
                    //cout << "..samtools should be installed to be able to read BAM files; will use the following command for samtools: "<<pathToSamtools_ + " view "+mateFileName<<"\n";
                    cout << "..samtools should be installed to be able to read BAM files; will use the following command for samtools: "<< command <<"\n";
                    }