X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=0c6ebe2de76c957f2a3f9c072b9127efb002e5fb;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=93adb7bf53b280892715411c66aedcf15b5c0df3;hpb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 93adb7b..0c6ebe2 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -28,9 +28,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.slayer";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute(); 
@@ -69,7 +70,7 @@ private:
 	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
 	#endif
 
-	bool abort, realign, trim, trimera, save, hasName, hasCount;
+	bool abort, realign, trim, trimera, save, hasName, hasCount, dups;
 	string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
 	int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
 	float divR;