1 #ifndef GETREPSEQSCOMMAND_H
2 #define GETREPSEQSCOMMAND_H
7 * Created by Sarah Westcott on 5/19/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "listvector.hpp"
23 class GetRepSeqsCommand : public Command {
31 GlobalData* globaldata;
37 string filename, fastafile, namesfile;
38 map<string, ofstream*> filehandles;
39 map<string, ofstream*>::iterator it;
40 map<string, bool> used; //group, if it had any unique otus
41 map<string, bool>::iterator it2;
42 map<string, string> seq;
43 map<string, string>::iterator it3;
47 void removeFiles(string);