added modify names parameter to set.dir

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index c8f20f10eed04c59df0aa27c136029e43713579e..85b6a8fdcbacf1ca1ee5b471b2142480ecf5da48 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1681,7 +1681,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                                        // get rest of line in case there is a primer name
                                        while (!in.eof())       {       
                                                char c = in.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
@@ -1713,7 +1713,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     group = "";
                     while (!in.eof())  {       
                                                char c = in.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        }