private:
- string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax;
+ string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax, picrustOtuFile;
vector<string> outputNames, Groups, sampleMetadata;
set<string> labels;
bool abort, allLines, picrust;
int getBiom(vector<SharedRAbundVector*>&);
- vector<string> getMetaData(vector<SharedRAbundVector*>&, vector<string>&);
+ vector<string> getMetaData(vector<SharedRAbundVector*>&);
vector<string> parseTax(string tax, vector<string>& scores);
int getSampleMetaData(vector<SharedRAbundVector*>&);
+ //for picrust
+ int getGreenGenesOTUIDs(vector<SharedRAbundVector*>&, map<string, string>&);
+ map<string, string> readGGOtuMap();
};