- int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, vector<string> revP, vector<string> li, vector<string> spa, map<int, oligosPair> pbr, map<int, oligosPair> ppr, bool po,
- vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
- int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,
+ int pd, int bd, int ld, int sd, int td, string o, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
+ int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage, bool lt,