#include "command.hpp"
#include "chimera.h"
-
/***********************************************************/
class ChimeraSlayerCommand : public Command {
public:
ChimeraSlayerCommand(string);
- ~ChimeraSlayerCommand();
- int execute();
- void help();
+ ChimeraSlayerCommand();
+ ~ChimeraSlayerCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.slayer"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
-
private:
struct linePair {
vector<int> processIDS; //processid
vector<linePair*> lines;
- int driver(linePair*, string, string, string);
- int createProcesses(string, string, string);
+ 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&, vector<unsigned long int>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
- bool abort, realign;
- string fastafile, templatefile, outputDir, search;
+ bool abort, realign, trim, trimera;
+ 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;
vector<string> outputNames;
vector<string> fastaFileNames;
+ vector<string> nameFileNames;
};