vector<string> setParameters();
string getCommandName() { return "classify.seqs"; }
string getCommandCategory() { return "Phylotype Analysis"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
string getDescription() { return "classify sequences"; }
bool abort, probs, save, flip;
int driver(linePair*, string, string, string, string);
- void appendTaxFiles(string, string);
int createProcesses(string, string, string, string);
string addUnclassifieds(string, int);