From bbbaf9ad20fc2190da7e852ead61328b70cecf00 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 5 Mar 2013 09:06:02 -0500
Subject: [PATCH] Revert push from stable (I forgot that pushing from stable
 overwrites current unstable changes)

---
 .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 45162fdba..e3d3c6640 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -397,7 +397,7 @@ public class PairHMMIndelErrorModel {
 
                         if (previousHaplotypeSeen == null) {
                             //no need to reallocate arrays for each new haplotype, as length won't change
-                            pairHMM.initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH);
+                            pairHMM.initialize(Y_METRIC_LENGTH, X_METRIC_LENGTH);
                         }
 
                         int startIndexInHaplotype = 0;