#include "mothur.h"
#include "command.hpp"
#include "chimera.h"
-
+#include "referencedb.h"
/***********************************************************/
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
-
+ ReferenceDB* rdb;
+
struct linePair {
unsigned long int start;
unsigned long int end;
int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
- bool abort, filter;
+ bool abort, filter, save;
string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
int processors, window, increment, numSeqs, templateSeqsLength;
Chimera* chimera;