diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java b/archive/java/src/org/broadinstitute/sting/BaseTransitionTableCalculatorJavaWalker.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java
rename to archive/java/src/org/broadinstitute/sting/BaseTransitionTableCalculatorJavaWalker.java
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
index 17a6ae126..58632c708 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
@@ -80,7 +80,6 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
 
     public void initialize() {
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
-        uac.baseModel = BaseMismatchModel.THREE_STATE;
         uac.ALL_BASES_MODE = true;
         ug = new UnifiedGenotyperEngine(getToolkit(), uac);