X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chopseqscommand.h;h=a9cfc102fb957ea775b14211db4e1f1e1118c50f;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=c9a4962c96fe9e548b50db1e4c0d6f63d1cdfff4;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index c9a4962..a9cfc10 100644
--- 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;