diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
index 1a7b4da51..a61614481 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
@@ -102,17 +102,24 @@ public class AlleleBiasedDownsamplingUtils {
     }
 
     private static int scoreAlleleCounts(final int[] alleleCounts) {
-        final int maxIndex = MathUtils.maxElementIndex(alleleCounts);
-        final int maxCount = alleleCounts[maxIndex];
+        if ( alleleCounts.length < 2 )
+            return 0;
 
-        int nonMaxCount = 0;
-        for ( int i = 0; i < 4; i++ ) {
-            if ( i != maxIndex )
-                nonMaxCount += alleleCounts[i];
-        }
+        // sort the counts (in ascending order)
+        final int[] alleleCountsCopy = alleleCounts.clone();
+        Arrays.sort(alleleCountsCopy);
 
-        // try to get the best score: in the het case the counts should be equal and in the hom case the non-max should be zero
-        return Math.min(Math.abs(maxCount - nonMaxCount), Math.abs(nonMaxCount));
+        final int maxCount = alleleCountsCopy[alleleCounts.length - 1];
+        final int nextBestCount = alleleCountsCopy[alleleCounts.length - 2];
+
+        int remainderCount = 0;
+        for ( int i = 0; i < alleleCounts.length - 2; i++ )
+            remainderCount += alleleCountsCopy[i];
+
+        // try to get the best score:
+        //    - in the het case the counts should be equal with nothing else
+        //    - in the hom case the non-max should be zero
+        return Math.min(maxCount - nextBestCount + remainderCount, Math.abs(nextBestCount + remainderCount));
     }
 
     /**
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
index 7c2f5619a..be19d3ef4 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
@@ -95,7 +95,7 @@ public class AlleleBiasedDownsamplingUtilsUnitTest extends BaseTest {
         actualCounts[3] += addT;
 
         final int[] results = AlleleBiasedDownsamplingUtils.runSmartDownsampling(actualCounts, (int)(pileupSize * contaminationFraction));
-        Assert.assertTrue(countsAreEqual(actualCounts, targetCounts));
+        Assert.assertTrue(countsAreEqual(results, targetCounts));
     }
 
     private static boolean countsAreEqual(final int[] counts1, final int[] counts2) {