working on sra and get.mimarkspackage commands. added file parameter to cluster...

[mothur.git] / getmimarkspackagecommand.h

diff --git a/getmimarkspackagecommand.h b/getmimarkspackagecommand.h
index e45dfe738af3c435a15619d39a8feb75b6613568..8bd2e4973c624eaa83d735c349a833181a39daea 100644 (file)
--- a/getmimarkspackagecommand.h
+++ b/getmimarkspackagecommand.h
@@ -32,10 +32,14 @@ public:
     void help() { m->mothurOut(getHelpString()); }
     
 private:
-    bool abort;
-    string oligosfile, groupfile, package;
+    bool abort, requiredonly;
+    string oligosfile, groupfile, package, inputfile, file;
     string outputDir;
-    vector<string> outputNames;
+    vector<string> outputNames, Groups;
+    set<string> uniqueNames;
+    
+    int readOligos();
+    int readFile();
 };
 
 /**************************************************************************************************/