+ vector<string> setParameters();
+ string getCommandName() { return "cluster.split"; }
+ string getCommandCategory() { return "Clustering"; }
+ 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/Cluster.split"; }
+ string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
vector<string> cluster(vector< map<string, string> >, set<string>&);
int mergeLists(vector<string>, map<float, int>, ListVector*);
map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
vector<string> cluster(vector< map<string, string> >, set<string>&);
int mergeLists(vector<string>, map<float, int>, ListVector*);
map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);