working on current change

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 6f7657f3da640514fb5125527b17cfd779a5cad0..5888feedcf5f6d6c01438d5acecc5e65ba897c54 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -116,7 +116,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                                inFastaName = m->getFastaFile(); 
                                if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " 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(inFastaName); } 
                        
                        //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"){  
@@ -127,6 +127,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                        oldNameMapFName = validParameter.validFile(parameters, "name", true);
                        if (oldNameMapFName == "not open") { abort = true; }
                        else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
+                       else { m->setNameFile(oldNameMapFName); }
                }
 
        }