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"
16 #include "counttable.h"
18 class ConsensusSeqsCommand : public Command {
20 ConsensusSeqsCommand(string);
21 ConsensusSeqsCommand();
22 ~ConsensusSeqsCommand(){}
24 vector<string> setParameters();
25 string getCommandName() { return "consensus.seqs"; }
26 string getCommandCategory() { return "Sequence Processing"; }
27 string getOutputFileNameTag(string, string);
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
30 string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
34 void help() { m->mothurOut(getHelpString()); }
40 string fastafile, listfile, namefile, countfile, label, outputDir;
42 vector<string> outputNames;
43 map<string, string> fastaMap;
44 map<string, string> nameMap;
45 map<string, int> nameFileMap;
46 int cutoff, seqLength;
50 int processList(ListVector*&);
51 string getConsSeq(string, ofstream&, int);
52 char getBase(vector<int>, int);