1 #ifndef CHIMERACOMMAND_H
2 #define CHIMERACOMMAND_H
8 * Created by Sarah Westcott on 6/29/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
18 /***********************************************************/
20 class ChimeraSeqsCommand : public Command {
22 ChimeraSeqsCommand(string);
23 ~ChimeraSeqsCommand();
31 string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile;
32 bool filter, correction, svg, printAll;
33 int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity;
40 /***********************************************************/