From d3f2bc43613971d3d9c1adb65c451270cea571ce Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 23 Mar 2012 13:51:00 -0400
Subject: [PATCH] Pre-allocate 10 alt alleles worth of PLs in the cache for
 efficiency.  This effectively means that we never need to re-allocate the
 cache in the future because we can't ever really handle that many alt
 alleles.

---
 .../sting/utils/variantcontext/GenotypeLikelihoods.java     | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

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 ae3dff9ed..1f3aead07 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -222,7 +222,10 @@ public class GenotypeLikelihoods {
     /*
      * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
      */
-    private static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = new GenotypeLikelihoodsAllelePair[]{ new GenotypeLikelihoodsAllelePair(0, 0) };
+    private static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex;
+    static {
+        calculatePLcache(65); // start with data for 10 alternate alleles
+    }
 
     private static void calculatePLcache(final int minIndex) {
         // how many alternate alleles do we need to calculate for?
@@ -266,6 +269,7 @@ public class GenotypeLikelihoods {
      */
     public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
         // make sure that we've cached enough data
+        // TODO -- this is not thread-safe!
         if ( PLindex >= PLIndexToAlleleIndex.length )
             calculatePLcache(PLindex);