added count parameter to chimera.slayer command

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 27bafd530cad4a66ef22e41696eef7e2328bde97..b7fbf4342b821d1f6eb6dbb7094d94c3e85d19a3 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }
@@ -59,9 +60,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;