#include "maligner.h"
#include "slayer.h"
-/***********************************************************************/
+//***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
class ChimeraSlayer : public Chimera {
public:
- ChimeraSlayer(string, bool, string);
+ ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
~ChimeraSlayer();
int getChimeras(Sequence*);
- void print(ostream&);
+ int print(ostream&, ostream&);
void printHeader(ostream&);
- void doPrep();
+ int doPrep();
+
+ #ifdef USE_MPI
+ int print(MPI_File&, MPI_File&);
+ #endif
private:
Sequence* querySeq;
vector<data_struct> chimeraResults;
string chimeraFlags, searchMethod, fastafile;
bool realign;
+ int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+ float divR;
void printBlock(data_struct, ostream&);
+ string getBlock(data_struct);
};