#include "mothur.h"
#include "command.hpp"
#include "chimera.h"
+#include "chimeracheckrdp.h"
/***********************************************************/
class ChimeraCheckCommand : public Command {
public:
ChimeraCheckCommand(string);
+ ChimeraCheckCommand();
~ChimeraCheckCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(long int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
vector<int> processIDS; //processid
vector<linePair*> lines;
int createProcesses(string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
bool abort, svg;
string fastafile, templatefile, namefile, outputDir;
int processors, increment, ksize, numSeqs, templateSeqsLength;
Chimera* chimera;
-
-
+ vector<string> fastaFileNames;
+ vector<string> nameFileNames;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
};
/***********************************************************/