X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=96fcb7d6799358ff4e10f930d1ad4165763b46a0;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=fe77cf08f34e3760734fb7b70568c4db09d603a2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index fe77cf0..96fcb7d 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -23,17 +23,22 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "parse.fastq";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+	string getDescription()		{ return "reads a fastq file and creates a fasta and quality file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }		
 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