From ab288354e9a6e9c726e285bcfafc103476eec16b Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 23 Mar 2012 10:47:01 -0400
Subject: [PATCH] Better error message for malformed input recal file.

---
 .../gatk/walkers/variantrecalibration/ApplyRecalibration.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index fac5b22aa..6b36f4e1b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -184,6 +184,8 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             }
         } catch ( FileNotFoundException e ) {
             throw new UserException.CouldNotReadInputFile(RECAL_FILE, e);
+        } catch ( Exception e ) {
+            throw new UserException.MalformedFile(RECAL_FILE, "Could not parse LOD and annotation information in input recal file. File is somehow malformed.");
         }
 
     }