X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=06ea359e6740bd822691e9f8ab6e3e53454cc724;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=9509a20af2528392c2df8590aea61fef6a7665b4;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9509a20..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;
@@ -166,7 +168,7 @@ int ParseFastaQCommand::execute(){
 			
 			//sanity check sequence length and number of quality scores match
 			if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
-			if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+			if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 			
 			//print sequence info to files
 			if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
@@ -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]);