string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Classify.otu"; }
-
+ 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"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
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