X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckcommand.h;h=8981a14ff5e6e7813ab54123fe3fa1c8b68a0bc4;hp=d29744ba39ba1791e27c306c7fd09f950ac15c0f;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index d29744b..8981a14 100644
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -27,7 +27,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.check";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
@@ -38,9 +40,9 @@ public:
 private:
 
 	struct linePair {
-		unsigned long int start;
-		unsigned long int end;
-		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 	};
 
 	vector<int> processIDS;   //processid
@@ -50,10 +52,10 @@ private:
 	int createProcesses(string, string);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
 	#endif
 
-	bool abort, svg;
+	bool abort, svg, save;
 	string fastafile, templatefile, namefile, outputDir;
 	int processors, increment, ksize, numSeqs, templateSeqsLength;
 	Chimera* chimera;