X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerapintailcommand.h;h=fa195e7253e870f2a38b8e72ca90a1a6875e4652;hp=9e1d6f8d253e61cc22e208eaf4d68259c06d7b02;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=65b6a38d00b3a72021611211e7c25392022c69ed

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 9e1d6f8..fa195e7 100644
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -28,7 +28,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.pintail";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
@@ -38,9 +40,9 @@ private:
 	ReferenceDB* rdb;
 	
 	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
@@ -50,7 +52,7 @@ 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, save;