X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=d8ebe50fb11859367256a28286dec9789cc70d36;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=253e03e2a1d380cb4d13f360fc9a5fecaaeb0808;hpb=8977d23b7f18d981b14e59c210c97198541ca7b0;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e..d8ebe50 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,7 +176,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 				if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
-			else if (queryFileName == "not open") { abort = true; }	
+			else if (queryFileName == "not open") { queryFileName = ""; abort = true; }	
 			else { m->setFastaFile(queryFileName); }
 			
 			referenceFileName = validParameter.validFile(parameters, "reference", true);
@@ -213,7 +213,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found") { temp = "1.00"; }
-			convert(temp, threshold);  
+			m->mothurConvert(temp, threshold);  
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -242,10 +242,15 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 
 			substitutionMatrix.resize(6);
 			for(int i=0;i<6;i++){	substitutionMatrix[i].resize(6,0);	}
+			
+			if ((namesFileName == "") && (queryFileName != "")){
+				vector<string> files; files.push_back(queryFileName); 
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {