ListVector* list;
InputData* input;
string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
- bool abort, allLines, probs;
+ bool abort, allLines, probs, persample;
int cutoff;
set<string> labels; //holds labels to be used
- vector<string> outputNames;
+ vector<string> outputNames, groups;
map<string, string> nameMap;
map<string, string> taxMap;
int process(ListVector*);
string addUnclassifieds(string, int);
- vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin
+ vector<string> findConsensusTaxonomy(vector<string>, int&, string&); // returns the name of the "representative" taxonomy of given bin
};