#include "mothur.h"
#include "command.hpp"
#include "chimera.h"
-
+#include "referencedb.h"
/***********************************************************/
ChimeraPintailCommand(string);
ChimeraPintailCommand();
- ~ChimeraPintailCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~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 int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ 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
int createProcesses(string, string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
#endif
- bool abort, filter;
+ bool abort, filter, save;
string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
int processors, window, increment, numSeqs, templateSeqsLength;
Chimera* chimera;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
vector<string> fastaFileNames;
-
-
};
/***********************************************************/