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[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 94c2bf5c1a392a8f12398db3806a503cd099f3bc..482bf7b5c2a67e57aaefc4cf4fc93c76a2b78611 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -205,6 +205,8 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }