1 #ifndef DECONVOLUTECOMMAND_H
2 #define DECONVOLUTECOMMAND_H
7 * Created by Sarah Westcott on 1/21/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
15 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
16 containing 2 columns. The first being the groupname and the second the list of identical sequence names. */
19 class DeconvoluteCommand : public Command {
22 DeconvoluteCommand(string);
24 ~DeconvoluteCommand() {}
26 vector<string> setParameters();
27 string getCommandName() { return "unique.seqs"; }
28 string getCommandCategory() { return "Sequence Processing"; }
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
31 string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
35 void help() { m->mothurOut(getHelpString()); }
39 string inFastaName, oldNameMapFName, outputDir;
40 vector<string> outputNames;