diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
index d22c0bd7b..20e3736f2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
@@ -44,7 +44,7 @@ public class MisencodedBaseQualityReadTransformer extends ReadTransformer {
 
     private boolean disabled;
     private boolean fixQuals;
-    private static int currentReadCounter = 0;
+    protected static int currentReadCounter = 0;
 
     @Override
     public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) {
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java
index 3b2696554..7a23f0f10 100644
--- a/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java
@@ -49,6 +49,8 @@ public class MisencodedBaseQualityUnitTest extends BaseTest {
 
     @BeforeMethod
     public void before() {
+        // reset the read counter so that we are deterministic
+        MisencodedBaseQualityReadTransformer.currentReadCounter = 0;
         header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
     }