1 #ifndef COuNTSEQSCOMMAND_H
2 #define COuNTSEQSCOMMAND_H
8 * Created by westcott on 6/1/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 class CountSeqsCommand : public Command {
19 CountSeqsCommand(string);
23 vector<string> setParameters();
24 string getCommandName() { return "count.seqs"; }
25 string getCommandCategory() { return "Sequence Processing"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
30 string getDescription() { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
33 void help() { m->mothurOut(getHelpString()); }
37 string namefile, groupfile, outputDir, groups;
39 vector<string> Groups, outputNames;
41 int processSmall(string);
42 int processLarge(string);
43 map<int, string> processNameFile(string);
44 map<int, string> getGroupNames(string, set<string>&);