X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=b4d90e542a98f329dd166a93c54d57852e0f54dd;hb=3504e4e2feeb05aabb0c79aa42cb696522030924;hp=60524566b2a4f02e4571c38d0602980e676d8138;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 6052456..b4d90e5 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -23,7 +23,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "parse.fastq";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
 	string getDescription()		{ return "reads a fastq file and creates a fasta and quality file"; }
 
@@ -33,10 +35,11 @@ public:
 private:
 
 	vector<string> outputNames;	
-	string outputDir, fastaQFile;
-	bool abort;
+	string outputDir, fastaQFile, format;
+	bool abort, fasta, qual;
 	
 	vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif