sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / shhhercommand.h

diff --git a/shhhercommand.h b/shhhercommand.h
index 9820ccef15f6db94747913eda42e468dba771064..c787fe41d5c0f2a30975feb9461bdaa3194aae18 100644 (file)
--- 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>&);