#include "command.hpp"
#include "chimera.h"
-
/***********************************************************/
class ChimeraSlayerCommand : public Command {
int driver(linePair*, string, string, string, string);
int createProcesses(string, string, string, string);
int divideInHalf(Sequence, string&, string&);
+ map<string, int> sortFastaFile(string, string);
#ifdef USE_MPI
int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
bool abort, realign, trim, trimera;
- string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
+ string fastafile, templatefile, outputDir, search, namefile;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;
Chimera* chimera;