fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 9ac7c5bcef6fee9c8e01b7838a3560f3478c5fcc..d8ebe50fb11859367256a28286dec9789cc70d36 100644 (file)
--- 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);
@@ -246,6 +246,11 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 
                        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) {