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[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
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+#ifndef CHIMERAPINTAILCOMMAND_H
+#define CHIMERAPINTAILCOMMAND_H
+
+/*
+ *  chimerapintailcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 4/1/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "command.hpp"
+#include "chimera.h"
+#include "referencedb.h"
+
+/***********************************************************/
+
+class ChimeraPintailCommand : public Command {
+
+public:
+
+       ChimeraPintailCommand(string);
+       ChimeraPintailCommand();
+       ~ChimeraPintailCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.pintail";             }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       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"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
+private:
+       ReferenceDB* rdb;
+       
+       struct linePair {
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+       };
+
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
+       
+       int driver(linePair*, string, string, string);
+       int createProcesses(string, string, string);
+       
+       #ifdef USE_MPI
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
+       #endif
+
+       bool abort, filter, save;
+       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
+       int processors, window, increment, numSeqs, templateSeqsLength;
+       Chimera* chimera;
+       vector<string> outputNames;
+       vector<string> fastaFileNames;
+};
+
+/***********************************************************/
+
+#endif
+
+