vector<Calculator*> sumCalculators;
InputData* input;
- bool abort, allLines, mult, all, createPhylip;
+ bool abort, allLines, mult, all, createPhylip, subsample;
set<string> labels; //holds labels to be used
- string label, calc, groups, sharedfile;
+ string label, calc, groups, sharedfile, output;
vector<string> Estimators, Groups, outputNames;
vector<SharedRAbundVector*> lookup;
string format, outputDir;
- int numGroups, processors;
+ int numGroups, processors, subsampleSize, iters;
int process(vector<SharedRAbundVector*>, string, string);
int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
+ int printSims(ostream&, vector< vector<double> >&);
};