X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.cpp;h=0f6e030bb0d1fec3f7cf99614fa0827c66de2bb5;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=995dc6606d86963d64d1bee857233c9656836da6;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 995dc66..0f6e030 100644
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -37,7 +37,7 @@ string MakeFastQCommand::getHelpString(){
 		helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
 		helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
 		helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -65,6 +65,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -115,7 +116,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
 				fastafile = m->getFastaFile(); 
 				if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setFastaFile(fastafile); }	
 			
 			qualfile = validParameter.validFile(parameters, "qfile", true);
 			if (qualfile == "not open") { abort = true; qualfile = ""; }
@@ -123,7 +124,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
 				qualfile = m->getQualFile(); 
 				if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setQualFile(qualfile); }	
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(fastafile);		}
@@ -180,7 +181,7 @@ int MakeFastQCommand::execute(){
 		qFile.close();
 		out.close();
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -200,7 +201,7 @@ 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;