X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=1331b7f47f4e131cb5a76913889d275b7ec93121;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=9509a20af2528392c2df8590aea61fef6a7665b4;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9509a20..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);	}
@@ -166,7 +190,7 @@ 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 +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]);