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();
22 vector<string> getRequiredParameters();
23 vector<string> getValidParameters();
24 vector<string> getRequiredFiles();
25 map<string, vector<string> > getOutputFiles() { return outputTypes; }
32 string fastafile, listfile, namefile, label, outputDir;
34 vector<string> outputNames;
35 map<string, vector<string> > outputTypes;
36 map<string, string> fastaMap;
37 map<string, string> nameMap;
38 map<string, string> nameFileMap;
42 int processList(ListVector*&);
43 string getConsSeq(string, ofstream&, string&, int);
44 char getBase(vector<int>);