X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.cpp;h=c6dcf2c83092303abdd685848efe9c875ca75976;hb=f320651dfb5359e6bba597280753553de28a2154;hp=8e1a7f52882fe1cf8e3b12a60538915306dacb46;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 8e1a7f5..c6dcf2c 100644
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -46,6 +46,26 @@ string MakeFastQCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MakeFastQCommand::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 == "fastq")             {   outputFileName =  "fastq";         }
+            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, "MakeFastQCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 MakeFastQCommand::MakeFastQCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -145,7 +165,7 @@ int MakeFastQCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		
-		string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
+		string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
 		outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
 		
 		ofstream out;
@@ -201,7 +221,7 @@ string MakeFastQCommand::convertQual(vector<int> qual) {
 	try {
 		string qualScores;
 		
-		int controlChar = int('!');
+		int controlChar = int('@');
 		
 		for (int i = 0; i < qual.size(); i++) { 
 			int temp = qual[i] + controlChar;