public:
- Slayer(int, int, int, float, int);
+ Slayer(int, int, int, float, int, int);
~Slayer() {};
string getResults(Sequence*, vector<Sequence*>);
private:
- int windowSize, windowStep, parentFragmentThreshold, iters;
+ int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
float divRThreshold;
vector<data_struct> outputResults;
+ vector< map<int, int> > baseSpots;
map<int, int> verticalFilter(vector<Sequence*>);
float computePercentID(string, string, int, int);
- vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
+ vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*, map<int, int>&);
vector<snps> getSNPS(string, string, string, int, int);
- void bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+ int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
float snpQA(vector<snps>);
float snpQB(vector<snps>);
float snpAB(vector<snps>);
+ MothurOut* m;
};