added modify names parameter to set.dir

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index c9a4962c96fe9e548b50db1e4c0d6f63d1cdfff4..a9cfc102fb957ea775b14211db4e1f1e1118c50f 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -27,7 +27,7 @@ class ChopSeqsCommand : public Command {
                string getCommandCategory()             { return "Sequence Processing"; }
                
         string getHelpString();        
-    string getOutputPattern(string);   
+        string getOutputPattern(string);       
                string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
                string getDescription()         { return "trim sequence length"; }
        
@@ -41,7 +41,7 @@ class ChopSeqsCommand : public Command {
             linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         };
     
-               string fastafile, outputDir, keep;
+               string fastafile, outputDir, keep, namefile, groupfile, countfile;
                bool abort, countGaps, Short;
                int numbases, processors;
                vector<string> outputNames;