X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsefastaqcommand.h;h=5ae6b9c482fe6b4022bb4d4c5d4ae2e79ea3aad8;hp=4481b98bb23bdbcd47a6059b2df0904c176ae9bf;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 4481b98..5ae6b9c 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -21,10 +21,11 @@ public:
 	~ParseFastaQCommand() {}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "parse.fastq";		}
+	string getCommandName()			{ return "fastq.info";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	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"; }
 
@@ -34,10 +35,11 @@ public:
 private:
 
 	vector<string> outputNames;	
-	string outputDir, fastaQFile;
-	bool abort, fasta, qual;
+	string outputDir, fastaQFile, format;
+	bool abort, fasta, qual, pacbio;
 	
 	vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif