X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=e4615ee8787d481dfad122bd8120ae35e130cdb6;hb=058715887611e00dc18324cb0bd4a4a8472530b3;hp=58e1656e6b995ae97d879863c0f2becc092ef9d1;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 58e1656..e4615ee 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,7 +15,7 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
@@ -23,7 +23,7 @@
 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*);
@@ -31,6 +31,10 @@ class ChimeraSlayer : public Chimera {
 		void printHeader(ostream&);
 		int doPrep();
 		
+		#ifdef USE_MPI
+		int print(MPI_File&, MPI_File&);
+		#endif
+		
 	private:
 		Sequence* querySeq;
 		DeCalculator* decalc;
@@ -43,8 +47,11 @@ class ChimeraSlayer : public Chimera {
 		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&);
+		void printBlock(data_struct, string, ostream&);
+		string getBlock(data_struct, string);
 		
 };