vector<string> setParameters();
string getCommandName() { return "remove.rare"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
void help() { m->mothurOut(getHelpString()); }
private:
- string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+ string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
int nseqs, allLines;
bool abort, byGroup;
vector<string> outputNames, Groups;