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[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 95604fc4ff4f738dc780de23b01ab65d4f473fe7..5da0ee8d0f091b8ce07acdedd48d2069e53ec1e9 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,6 +224,8 @@ AlignCommand::AlignCommand(string option)  {
                                                        //erase from file list
                                                        candidateFileNames.erase(candidateFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(candidateFileNames[i]);
                                                }
                                        }
                                }