X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=06ea359e6740bd822691e9f8ab6e3e53454cc724;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=730873a4bd64e5409c5e3580bfd15338179a787c;hpb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;p=mothur.git

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 730873a..06ea359 100644
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -33,8 +33,10 @@ string ParseFastaQCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
-		helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+		helpString += "The fastq.info command parameters are fastq, fasta and qfile; fastq is required.\n";
 		helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+        helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
+        helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
 		helpString += "Example fastq.info(fastaq=test.fastaq).\n";
 		helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
 		return helpString;
@@ -214,7 +216,7 @@ vector<int> ParseFastaQCommand::convertQual(string qual) {
 	try {
 		vector<int> qualScores;
 		
-		int controlChar = int('!');
+		int controlChar = int('@');
 		
 		for (int i = 0; i < qual.length(); i++) { 
 			int temp = int(qual[i]);