vector<string> setParameters();
string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
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 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
string getDescription() { return "find the concensus taxonomy for each OTU"; }
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
};