vector<string> setParameters();
string getCommandName() { return "cluster.split"; }
string getCommandCategory() { return "Clustering"; }
- 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/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
- bool print_start, abort, hard, large, classic;
+ bool print_start, abort, hard, large, classic, runCluster;
time_t start;
ofstream outList, outRabund, outSabund;