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();
33 linePair(long int i, int j) : start(i), numSeqs(j) {}
35 vector<int> processIDS; //processid
36 vector<linePair*> lines;
38 int driver(linePair*, string, string, string);
39 int createProcesses(string, string, string);
40 void appendOutputFiles(string, string);
43 string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir, search;
44 bool filter, correction, svg, printAll, realign;
45 int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
52 /***********************************************************/