1 #ifndef CHIMERAUCHIMECOMMAND_H
2 #define CHIMERAUCHIMECOMMAND_H
6 * chimerauchimecommand.h
9 * Created by westcott on 5/13/11.
10 * Copyright 2011 Schloss Lab. All rights reserved.
15 #include "command.hpp"
17 /***********************************************************/
19 class ChimeraUchimeCommand : public Command {
21 ChimeraUchimeCommand(string);
22 ChimeraUchimeCommand();
23 ~ChimeraUchimeCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "chimera.uchime"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getHelpString();
29 string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
32 void help() { m->mothurOut(getHelpString()); }
35 vector<int> processIDS; //processid
36 int driver(string, string, string, string);
37 int createProcesses(string, string, string, string);
39 bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
40 string fastafile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
43 vector<string> outputNames;
44 vector<string> fastaFileNames;
45 vector<string> nameFileNames;
49 /***********************************************************/