X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraperseuscommand.h;h=b6957e39d45cc877a9bee28cccf933af6d86f49e;hb=f320651dfb5359e6bba597280753553de28a2154;hp=84563ac6ecc006ca7150f7f5e025b340da964fdf;hpb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;p=mothur.git

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 84563ac..b6957e3 100644
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -28,8 +28,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.perseus";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Chimera.perseus\n"; }
+	string getCitation() { return "Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.perseus\n"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute(); 
@@ -44,7 +45,7 @@ private:
 	
 	bool abort;
 	string fastafile, groupfile, outputDir, namefile;
-	int processors;
+	int processors, alignLength;
 	double cutoff, alpha, beta;
 	
 	vector<string> outputNames;
@@ -98,7 +99,7 @@ struct perseusData {
 	}
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){ 
 	perseusData* pDataArray;