From dc9b351b5e21e84b4296995ea97ae25427ab4a94 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 10 Nov 2011 17:10:26 -0500
Subject: [PATCH] Meaningful error message when an IntervalArg file fails to
 parse correctly

---
 .../broadinstitute/sting/commandline/IntervalBinding.java    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
index 86ca6c2df..f920d90ef 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
@@ -92,7 +92,10 @@ public final class IntervalBinding<T extends Feature> {
                 codec.readHeader(lineReader);
                 String line = lineReader.readLine();
                 while ( line != null ) {
-                    intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
+                    final Feature feature = codec.decodeLoc(line);
+                    if ( feature == null )
+                        throw new UserException.MalformedFile(featureIntervals.getSource(), "Couldn't parse line '" + line + "'");
+                    intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
                     line = lineReader.readLine();
                 }
             } catch (IOException e) {