X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=1331b7f47f4e131cb5a76913889d275b7ec93121;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=730873a4bd64e5409c5e3580bfd15338179a787c;hpb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;p=mothur.git

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 730873a..1331b7f 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;
@@ -44,6 +46,28 @@ string ParseFastaQCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fasta"; }
+            else if (type == "qfile") {  outputFileName =  "qual"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ParseFastaQCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){	
 	try {
@@ -130,8 +154,8 @@ int ParseFastaQCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//open Output Files
-		string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
-		string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
+		string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta");
+		string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
 		ofstream outFasta, outQual;
 		
 		if (fasta) { m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);	}
@@ -214,7 +238,7 @@ 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]);