fix closing of file at end of run

src/OutputByOrbit.cc

@@ -33,11 +33,18 @@ void OutputByOrbitStream::OutputFixedOrbits(Slice &out) {
         control.output_force_write) {  // i.e should be writing data
       n = fwrite(out.begin(), 1, out.size(),
                  output_file_handler_.getFile(control.run_number, index));
+      current_file_size += n;
+    } else if (output_file_handler_.hasFile()) {
+      // the run has been stopped so drop but first check if there is a last
+      // file to close
+      LOG(TRACE) << "the run was stopped. queueing the last file for close and "
+                    "rename ";
+      output_file_handler_.enqueue_current_file_for_close_and_move_maybe();
     }
-    current_file_size += n;
+
   } else {  // i.e should not currently be writing data - but then we should
             // never get here in the first place
-    output_file_handler_.enqueue_current_file_for_close_and_move_maybe();
+    LOG(TRACE) << "got an empty slice ";
   }
 }