added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / mergegroupscommand.h

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index dfd65adf1fdc9f7c6c84491f0714eff5cfd3888c..7f216ebed7653a2647c4770e4ce17e5e6d881e95 100644 (file)
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -26,6 +26,8 @@ public:
        string getCommandCategory()             { return "General";                     }
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+       string getDescription()         { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -36,10 +38,12 @@ private:
        
        bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
-       string groups, label, outputDir, inputDir, designfile, sharedfile;
+       string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
        vector<string> Groups, outputNames;
                
        int process(vector<SharedRAbundVector*>&, ofstream&);
+       int processSharedFile(GroupMap*&);
+       int processGroupFile(GroupMap*&);
 };
 
 #endif