X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=c5ef88885d9b4c1e7275c998e8a2b35bbbbba99b;hb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;hp=926326beb876087f1361278a9523759ab4bc3372;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 926326b..c5ef888 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -28,10 +28,11 @@ public:
 private:
 
 	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
+
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	
@@ -39,15 +40,17 @@ private:
 	int createProcesses(string, string, string);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
 	#endif
 
-	bool abort, realign, MPIWroteAccnos;
+	bool abort, realign;
 	string fastafile, templatefile, outputDir, search;
 	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;
 	
 };