1 #ifndef SPLITGROUPSCOMMAND_H
2 #define SPLITGROUPSCOMMAND_H
8 * Created by westcott on 9/20/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 /* split.groups - given a group file, split sequences and names files in to separate files *.group1.fasta and .group1.names. */
17 #include "command.hpp"
19 #include "sequence.hpp"
21 /***************************************************************************************/
23 class SplitGroupCommand : public Command {
26 SplitGroupCommand(string);
29 vector<string> getRequiredParameters();
30 vector<string> getValidParameters();
31 vector<string> getRequiredFiles();
32 map<string, vector<string> > getOutputFiles() { return outputTypes; }
41 vector<string> outputNames;
42 map<string, vector<string> > outputTypes;
43 map<string, vector<string> > nameMap;
44 map<string, vector<string> >::iterator itNames;
47 string outputDir, namefile, groupfile, groups, fastafile;
48 vector<string> Groups;
52 /***************************************************************************************/