X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerapintailcommand.h;h=fa195e7253e870f2a38b8e72ca90a1a6875e4652;hp=acb078173501a7d7cf48cc88f5c305e12eccc225;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index acb0781..fa195e7 100644
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
-
+#include "referencedb.h"
 
 /***********************************************************/
 
@@ -28,18 +28,21 @@ 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"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }		
 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
@@ -49,10 +52,10 @@ 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, consfile, quanfile, maskfile, outputDir, inputDir;
 	int processors, window, increment, numSeqs, templateSeqsLength;
 	Chimera* chimera;