1 #ifndef BINSEQCOMMAND_H
2 #define BINSEQCOMMAND_H
7 * Created by Sarah Westcott on 4/3/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 /* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
14 #include "command.hpp"
15 #include "inputdata.h"
16 #include "listvector.hpp"
20 class BinSeqCommand : public Command {
23 BinSeqCommand(string);
27 vector<string> setParameters();
28 string getCommandName() { return "bin.seqs"; }
29 string getCommandCategory() { return "Sequence Processing"; }
30 string getHelpString();
31 string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
32 string getDescription() { return "maps sequences to otus"; }
35 void help() { m->mothurOut(getHelpString()); }
44 set<string> labels; //holds labels to be used
45 string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
48 vector<string> outputNames;
51 int process(ListVector*);