X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.cpp;h=0f6e030bb0d1fec3f7cf99614fa0827c66de2bb5;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=2dd45a542665c71a1221adca4eed77d9c1bb65f5;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 2dd45a5..0f6e030 100644
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -116,7 +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 = ""; }
@@ -124,7 +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);		}
@@ -181,7 +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();
@@ -201,7 +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;