From 58eed20b8369f6b4905f669d52bbbd1e7977dcdf Mon Sep 17 00:00:00 2001
From: Kiran V Garimella <kiran@broadinstitute.org>
Date: Sat, 23 Jul 2011 01:00:46 -0400
Subject: [PATCH] Copy all entries from the attributes map, rather than
 attempting to modify an unmodifiable map.

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java        | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index fb5267369..12a657d7c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -266,7 +266,8 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
                 }
             }
 
-            Map<String, Object> attributes = bestChildGenotype.getAttributes();
+            Map<String, Object> attributes = new HashMap<String, Object>();
+            attributes.putAll(bestChildGenotype.getAttributes());
             attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
             bestChildGenotype = Genotype.modifyAttributes(bestChildGenotype, attributes);