From 4d9582de777f3f9c9543ed1102e6da7bee2c95e9 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 27 Feb 2012 14:02:26 -0500
Subject: [PATCH] More general catching of Exceptions in interval reading to
 throw MalformedFile exception in all cases

-- Now throws UserException no matter what happens during the reading of the intervals file.
---
 .../org/broadinstitute/sting/commandline/IntervalBinding.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
index 9e2c9a818..0c6096e0c 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
@@ -98,8 +98,8 @@ public final class IntervalBinding<T extends Feature> {
                     intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
                     line = lineReader.readLine();
                 }
-            } catch (IOException e) {
-                throw new UserException("Problem reading the interval file " + featureIntervals.getSource() + "; " + e.getMessage());
+            } catch (Exception e) {
+                throw new UserException.MalformedFile(featureIntervals.getSource(), "Problem reading the interval file", e);
             }
 
         } else {