From 53383e82ecd9e3de2d4506daee6dc4fae8e81773 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 16 Aug 2012 21:41:18 -0400
Subject: [PATCH] Hmm, not good.  Fixing the math in PBT resulted in changed
 MD5s for integration tests that look like significant changes.  I am
 reverting and will report this to Laurent.

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java         | 2 +-
 1 file changed, 1 insertion(+), 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 0dcafb30a..bbd4bf92f 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
@@ -645,7 +645,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
                                 bestChildGenotype.clear();
                                 bestChildGenotype.add(childGenotype.getKey());
                             }
-                            else if(MathUtils.compareDoubles(configurationLikelihood, bestConfigurationLikelihood) == 0) {
+                            else if(configurationLikelihood == bestConfigurationLikelihood) {
                                 bestFirstParentGenotype.add(firstParentGenotype.getKey());
                                 bestSecondParentGenotype.add(secondParentGenotype.getKey());
                                 bestChildGenotype.add(childGenotype.getKey());