X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraccodecommand.h;h=52bf07d01f6a411b870e119f82ef97f7b6f45cbd;hp=cedec2f690f6b3c981280d41a0f9bb59777ae015;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index cedec2f..52bf07d 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -26,8 +26,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.ccode";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
-	string getCitation() { return "Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez. http://www.mothur.org/wiki/Chimera.ccode"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -35,9 +38,9 @@ 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
 	vector<linePair*> lines;
@@ -46,10 +49,10 @@ private:
 	int createProcesses(string, string, string);
 	
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
 	#endif
 
-	bool abort, filter;
+	bool abort, filter, save;
 	string fastafile, templatefile, outputDir, maskfile;
 	int processors, window, numwanted, numSeqs, templateSeqsLength;
 	Chimera* chimera;