X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.h;h=c787fe41d5c0f2a30975feb9461bdaa3194aae18;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=9820ccef15f6db94747913eda42e468dba771064;hpb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;p=mothur.git

diff --git a/shhhercommand.h b/shhhercommand.h
index 9820cce..c787fe4 100644
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -40,9 +40,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "shhh.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Shhh.flows"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nQuince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009).  Accurate determination of microbial diversity from 454 pyrosequencing data.  Nat. Methods 6:639.\nhttp://www.mothur.org/wiki/Shhh.flows"; }
 	string getDescription()		{ return "shhh.flows"; }
 
 	
@@ -69,7 +70,7 @@ private:
     vector<string> flowFileVector;
 	
     vector<string> parseFlowFiles(string);
-    int driver(vector<string>, string, string, int, int);
+    int driver(vector<string>, string, string);
     int createProcesses(vector<string>);
     int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
     int getUniques(int, int, vector<short>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<short>&);