X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=96fcb7d6799358ff4e10f930d1ad4165763b46a0;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=071077577f1bec0fb39b05a6d18b01917e7a839e;hpb=2c5386dc0cb6a0e42e8d7256bd6fb18ab66e4480;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 0710775..96fcb7d 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -17,17 +17,28 @@ class ParseFastaQCommand : public Command {
 
 public:
 	ParseFastaQCommand(string);
-	~ParseFastaQCommand();
-	int execute();
-	void help();	
+	ParseFastaQCommand();
+	~ParseFastaQCommand() {}
 	
+	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