From 344a938a70de7407ca1169171060e92f3cf11777 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sun, 18 Mar 2012 00:36:30 -0400
Subject: [PATCH] When checking to make sure that we have cached enough data in
 the PL array, use the converted index value since that's what will be used as
 an index into the array.

---
 .../utils/variantcontext/GenotypeLikelihoods.java      | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index cc0d9788b..ae3dff9ed 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -288,11 +288,13 @@ public class GenotypeLikelihoods {
      * @return the allele index pair
      */
     public static GenotypeLikelihoodsAllelePair getAllelePairUsingDeprecatedOrdering(final int PLindex) {
-        // make sure that we've cached enough data
-        if ( PLindex >= PLIndexToAlleleIndex.length )
-            calculatePLcache(PLindex);
+        final int convertedIndex = PLindexConversion[PLindex];
 
-        return PLIndexToAlleleIndex[PLindexConversion[PLindex]];
+        // make sure that we've cached enough data
+        if ( convertedIndex >= PLIndexToAlleleIndex.length )
+            calculatePLcache(convertedIndex);
+
+        return PLIndexToAlleleIndex[convertedIndex];
     }
 
     /**