From fd511d12a2143d83cdb931bad984a8b28d7a0254 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 13 Jan 2014 22:47:43 -0500
Subject: [PATCH] Fixing the Haplotype Resolver so that it doesn't complain
 about missing header lines.

The code comments very clearly state that INFO fields shouldn't be propagated into the output,
but someone must have accidentally changed it afterwards.  This is just a simple one-line fix
to make sure the code adhered to the comments.

Delivers #63333488.
---
 .../sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
index 01ab421b3..cfd07da67 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
@@ -258,7 +258,7 @@ public class HaplotypeResolver extends RodWalker<Integer, Integer> {
     }
 
     private void writeOne(final VariantContext vc, final String set, final String status) {
-        final Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
+        final Map<String, Object> attrs = new HashMap<>();
         if ( SET_KEY != null && set != null )
             attrs.put(SET_KEY, set);
         if ( STATUS_KEY != null && status != null )