1 #ifndef REMOVESEQSCOMMAND_H
2 #define REMOVESEQSCOMMAND_H
8 * Created by Sarah Westcott on 7/8/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
15 class RemoveSeqsCommand : public Command {
19 RemoveSeqsCommand(string);
21 ~RemoveSeqsCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "remove.seqs"; }
25 string getCommandCategory() { return "Sequence Processing"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
30 string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
33 void help() { m->mothurOut(getHelpString()); }
38 string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
40 vector<string> outputNames;
41 map<string, string> uniqueMap;