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[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 77377a47c34e51bf13e97bef11f7966ba2cb6199..ec043360ad1cd553d782d1d67ab531c9a4610778 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -157,7 +157,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found")        {       oligoFileName = "";             }
                        else if(temp == "not open")     {       abort = true;                   } 
-                       else                                            {       oligoFileName = temp;   }
+                       else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
                        
                        temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
                        else if(m->isTrue(temp))        {       fasta = 1;      }