X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=5ae6b9c482fe6b4022bb4d4c5d4ae2e79ea3aad8;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=fe77cf08f34e3760734fb7b70568c4db09d603a2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index fe77cf0..5ae6b9c 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -21,19 +21,25 @@ public:
 	~ParseFastaQCommand() {}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "parse.fastq";		}
+	string getCommandName()			{ return "fastq.info";		}
 	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"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }		
 private:
 
 	vector<string> outputNames;	
-	string outputDir, fastaQFile;
-	bool abort;
+	string outputDir, fastaQFile, format;
+	bool abort, fasta, qual, pacbio;
 	
 	vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif