X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=3ce4cce4b40cbe331b260f08552fa34bad010d3d;hb=c5f38b0c83719306fd2e5a7a83e04988b1853f62;hp=bf9cf7f8166884e1dda08f0de7a1989bec961c65;hpb=81276c241b984898f8d30ad123c00592ee6db7b8;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index bf9cf7f..3ce4cce 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
 /***********************************************************************/
 
@@ -23,13 +23,17 @@
 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;
@@ -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&);
+		string getBlock(data_struct);
 		
 };