public:
RemoveSeqsCommand(string);
- ~RemoveSeqsCommand(){};
- int execute();
- void help();
-
+ RemoveSeqsCommand();
+ ~RemoveSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "remove.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+ string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
vector<string> outputNames;
void readAccnos();
int readList();
int readTax();
+ int readQual();
};