1 #ifndef CHIMERAPINTAILCOMMAND_H
2 #define CHIMERAPINTAILCOMMAND_H
5 * chimerapintailcommand.h
8 * Created by westcott on 4/1/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
16 #include "referencedb.h"
18 /***********************************************************/
20 class ChimeraPintailCommand : public Command {
24 ChimeraPintailCommand(string);
25 ChimeraPintailCommand();
26 ~ChimeraPintailCommand(){}
28 vector<string> setParameters();
29 string getCommandName() { return "chimera.pintail"; }
30 string getCommandCategory() { return "Sequence Processing"; }
32 string getHelpString();
33 string getOutputPattern(string);
34 string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
35 string getDescription() { return "detect chimeric sequences"; }
38 void help() { m->mothurOut(getHelpString()); }
43 unsigned long long start;
44 unsigned long long end;
45 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
48 vector<int> processIDS; //processid
49 vector<linePair*> lines;
51 int driver(linePair*, string, string, string);
52 int createProcesses(string, string, string);
55 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
58 bool abort, filter, save;
59 string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
60 int processors, window, increment, numSeqs, templateSeqsLength;
62 vector<string> outputNames;
63 vector<string> fastaFileNames;
66 /***********************************************************/