From 6f78bf504116c1ec6c5abb6d55f0f67607de4928 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@roadinstitute.org>
Date: Tue, 28 Oct 2014 10:31:39 -0400
Subject: [PATCH] Catch RuntimeException and add the bad file name to the newly
 thown exception

---
 .../engine/datasources/rmd/ReferenceOrderedDataSource.java     | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
index c88b9b7f2..e90cb8047 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
@@ -244,9 +244,10 @@ class ReferenceOrderedQueryDataPool extends ResourcePool<RMDTrack,LocationAwareS
             }
         } catch (FileNotFoundException e) {
             throw new UserException.CouldNotReadInputFile(fileDescriptor.getName(), "it could not be found");
-        } catch (IOException e) {
+        } catch (IOException | RuntimeException e) {
             throw new ReviewedGATKException("Unable to create iterator for rod named " + fileDescriptor.getName(),e);
         }
+
     }
 
     @Override