X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.h;h=e3e0b70b087b17e5d6299052cb06567e9b7c9f69;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=946c990047fe8ad65f2fb332deb6e072534fc932;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/makefastqcommand.h b/makefastqcommand.h
index 946c990..e3e0b70 100644
--- a/makefastqcommand.h
+++ b/makefastqcommand.h
@@ -24,7 +24,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.fastq";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
+	string getDescription()		{ return "creates a fastq file from a fasta and quality file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -32,7 +37,7 @@ public:
 	
 private:
 	
-	string fastafile, qualfile, outputDir;
+	string fastafile, qualfile, outputDir, format;
 	bool abort;
 	vector<string> outputNames;