diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
rename to protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 80a787fe0..4cc152d53 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
index 6482354a9..1c227170d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
@@ -33,8 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -50,6 +49,9 @@ import java.io.PrintStream;
  */
 @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements TreeReducible<Long> {
+
+    public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
+
     // the possible diploid genotype strings
     private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
 
@@ -73,7 +75,7 @@ public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements Tre
 
         ReadBackedPileup pileup = context.getBasePileup().getPileupWithoutMappingQualityZeroReads();
         double likelihoods[] = getReferencePolarizedPriors(ref.getBase(),
-                UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY,
+                HUMAN_SNP_HETEROZYGOSITY,
                 0.01);
         // get the bases and qualities from the pileup
         byte bases[] = pileup.getBases();
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java
similarity index 98%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
rename to public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java
index 86047d30b..6d90038d7 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.genotyper;
+package org.broadinstitute.sting.utils.genotyper;
 
 import org.broadinstitute.variant.utils.BaseUtils;
 
diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
rename to public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
rename to public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java