1 #ifndef CONSENSUSSEQSCOMMAND_H
2 #define CONSENSUSSEQSCOMMAND_H
5 * consensusseqscommand.h
8 * Created by westcott on 11/23/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "listvector.hpp"
17 class ConsensusSeqsCommand : public Command {
19 ConsensusSeqsCommand(string);
20 ConsensusSeqsCommand();
21 ~ConsensusSeqsCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "consensus.seqs"; }
25 string getCommandCategory() { return "Sequence Processing"; }
26 string getHelpString();
27 string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
28 string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
32 void help() { m->mothurOut(getHelpString()); }
37 string fastafile, listfile, namefile, label, outputDir;
39 vector<string> outputNames;
40 map<string, string> fastaMap;
41 map<string, string> nameMap;
42 map<string, string> nameFileMap;
47 int processList(ListVector*&);
48 string getConsSeq(string, ofstream&, string&, int);
49 char getBase(vector<int>, int);