diff --git a/uk/ac/sanger/artemis/util/FileDocument.java b/uk/ac/sanger/artemis/util/FileDocument.java
index 365d34235cfa4e1c8bbc7a611114ea16bfbfbf94..9fb2200cffe9cdeb2f0ba2512e51ab7509b07c1a 100644
--- a/uk/ac/sanger/artemis/util/FileDocument.java
+++ b/uk/ac/sanger/artemis/util/FileDocument.java
@@ -115,6 +115,8 @@ public class FileDocument extends Document {
                                getProgressListeners ());;
     
     if (read_file.getName ().endsWith (".gz")) {
+      if(IndexedGFFDocumentEntry.isIndexed(read_file))
+        return new BlockCompressedInputStream(read_file);
       // assume this file is gzipped
       return new WorkingGZIPInputStream (file_input_stream);
     } else {