added end of file character to some type type reads. fixes while testing.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a103626f7dd9fbed1074f7132175651360bfe464..2c88bef2d036e798a0e84a85d0af1120c3fdd6df 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1533,7 +1533,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.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;  }
                                        }