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"
19 #include "counttable.h"
21 class BinSeqCommand : public Command {
24 BinSeqCommand(string);
28 vector<string> setParameters();
29 string getCommandName() { return "bin.seqs"; }
30 string getCommandCategory() { return "Sequence Processing"; }
32 string getHelpString();
33 string getOutputPattern(string);
34 string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
35 string getDescription() { return "maps sequences to otus"; }
38 void help() { m->mothurOut(getHelpString()); }
47 set<string> labels; //holds labels to be used
48 string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
51 vector<string> outputNames;
54 int process(ListVector*);