vector<string> setParameters();
string getCommandName() { return "remove.groups"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
- string getDescription() { return "removes sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+ string getDescription() { return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
+ string accnosfile, fastafile, namefile, groupfile, countfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
bool abort;
vector<string> outputNames, Groups;
GroupMap* groupMap;
int readShared();
int readName();
int readGroup();
- void readAccnos();
+ int readCount();
int readList();
int readTax();
int fillNames();
+ int readDesign();
};