From 7e1bfd6a7cdb1c6a721ccaa84475d52f7d2b5b89 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 5 Mar 2013 09:03:31 -0500
Subject: [PATCH] Included an accidental change from unstable into the previous
 push

---
 .../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 e3d3c6640..45162fdba 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(Y_METRIC_LENGTH, X_METRIC_LENGTH);
+                            pairHMM.initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH);
                         }
 
                         int startIndexInHaplotype = 0;