X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=4481b98bb23bdbcd47a6059b2df0904c176ae9bf;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=fe77cf08f34e3760734fb7b70568c4db09d603a2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index fe77cf0..4481b98 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -23,7 +23,11 @@ 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()); }		
@@ -31,7 +35,7 @@ private:
 
 	vector<string> outputNames;	
 	string outputDir, fastaQFile;
-	bool abort;
+	bool abort, fasta, qual;
 	
 	vector<int> convertQual(string);
 };