vector<string> setParameters();
string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
string getDescription() { return "find the concensus taxonomy for each OTU"; }
map<string, string> nameMap;
map<string, string> taxMap;
- int readNamesFile();
- int readTaxonomyFile();
- void removeConfidences(string&);
int process(ListVector*);
string addUnclassifieds(string, int);
vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin