From 2ba35dc7ba5af51a01c544bd0814cef7a6b7bdb1 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 23 Jan 2011 06:04:36 +0000
Subject: [PATCH] Bad chain files are user errors

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5059 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/LiftoverVariants.java  | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index be80ba4e5..56c5d8db3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -70,7 +70,12 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
     private long successfulIntervals = 0, failedIntervals = 0;
 
     public void initialize() {
-        liftOver = new LiftOver(CHAIN);
+        try {
+            liftOver = new LiftOver(CHAIN);
+        } catch (PicardException e) {
+            throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
+        }
+
         liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
 
         try {