X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerapintailcommand.h;h=fa195e7253e870f2a38b8e72ca90a1a6875e4652;hp=49912c69a243391311ba08f101f595da3e0c0c97;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 49912c6..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 getCitation() { return "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies' paper by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1. http://www.mothur.org/wiki/Chimera.pintail"; }
-
+    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;