Function findSmallestSuffix

src/myFunc.cpp:2397–2445

}

string findSmallestSuffix (string s1, string s2) {

    if (s1 == "")
        return  s2;

   // cout <<"s1: "<<s1<< "\ns2: "<<s2 << "\n";

    string suffix = "";
    vector<string>values1 = split(s1, ';');
    vector<string>values2 = split(s2, ';');

    int size1 = values1.size();
    int size2 = values2.size();

    //cout <<"s1 size: "<<size1<< "; s2 size: "<<size2 << "\n";

    int startSuffix = 0;

    for (int i=max(0,size1-size2); i<size1; i++) {

        if (values1[i].compare(values2[0])==0) {
        //found possible overlap
            int realOverlap = 1;

            for (int j=i+1; j<size1; j++) {
                if (values1[j].compare(values2[j-i])!=0) {
                    j=size1;
                    realOverlap=0;
                }
            }
            if (realOverlap) {
                startSuffix = size1 - i;
                i=size1;
            }
        }
    }
    if (startSuffix == 0)
        return s2;

    if (startSuffix >= size2) //should never happen
        return "";

    suffix = values2[startSuffix];
    for (int i=startSuffix+1; i<size2; i++) {
        suffix += ";"+ values2[i];
    }

    return suffix;
}

std::string getNormalBAFforPloidy(int ploidy) {
    if (ploidy>1) {