+ vector< vector<float> > wordGenusProb; //vector of maps from genus to probability
+ //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
+
+ vector<int> genusTotals;
+ vector<int> genusNodes; //indexes in phyloTree where genus' are located
+
+ vector<diffPair> WordPairDiffArr;
+
+ int kmerSize, numKmers, confidenceThreshold, iters;
+
+ string bootstrapResults(vector<int>, int, int);
+ int getMostProbableTaxonomy(vector<int>);
+ void readProbFile(ifstream&, ifstream&, string, string);
+ bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+ bool isReversed(vector<int>&);
+ vector<int> createWordIndexArr(Sequence*);
+ int generateWordPairDiffArr();