From 4d654f30d490e61a268c71996b56d35f73de96a2 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 4 Jun 2009 18:24:43 +0000
Subject: [PATCH] slightly improved error message printed upon failure to parse
 interval list file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@895 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 2adede24d..b872f9da7 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -594,6 +594,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
                 ret = parseGenomeLocs(locStr);
                 return ret;
             } catch (Exception e2) {
+            	logger.error("Attempt to parse interval file in GATK format failed: "+e2.getMessage());
                 e2.printStackTrace();
                 throw new StingException("Unable to parse out interval file in either format", e);
             }