diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
index e03f21334..b1d3e8a12 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
@@ -55,11 +55,13 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
     boolean DEBUGOUT = false;
 
     private HaplotypeIndelErrorModel model;
+    private ArrayList<Integer> sitesVisited;
 
     protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
         model = new HaplotypeIndelErrorModel(maxReadDeletionLength, insertionStartProbability,
                 insertionEndProbability, alphaDeletionProbability, HAPLOTYPE_SIZE, false, DEBUGOUT);
+        sitesVisited = new  ArrayList<Integer>();
     }
 
     public Allele getLikelihoods(RefMetaDataTracker tracker,
@@ -82,9 +84,15 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
         if (!vc.isIndel())
             return null;
 
+        if (sitesVisited.contains(new Integer(vc.getStart())))
+             return null;
+
+        sitesVisited.add(new Integer(vc.getStart()));
+
         if ( !(priors instanceof DiploidIndelGenotypePriors) )
              throw new StingException("Only diploid-based Indel priors are supported in the DINDEL GL model");
 
+
         int eventLength = vc.getReference().getBaseString().length() - vc.getAlternateAllele(0).getBaseString().length();
         // assume only one alt allele for now
         if (eventLength<0)
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 43d74a055..20b53c185 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -43,7 +43,9 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
     private boolean DEBUGOUT = false;
     private boolean SIMPLE_GREEDY_GENOTYPER = false;
-    
+    private static final double EPS = 1e-300;
+    private static final double LOGEPS = -300;
+
     protected ExactAFCalculationModel(int N, Logger logger, PrintStream verboseWriter) {
         super(N, logger, verboseWriter);
     }
@@ -60,15 +62,20 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
  
 
         alleleFrequencyPosteriors = updateAFEstimate(GLs, alleleFrequencyPriors);
-        double meanAF = computeMeanAF(alleleFrequencyPosteriors);
 
-        if (DEBUGOUT)
+        if (DEBUGOUT) {
+            double meanAF = computeMeanAF(alleleFrequencyPosteriors);
             System.out.format("Mean AF: %5.4f. PVariant: %5.5f\n", meanAF,1.0-alleleFrequencyPosteriors[0]);
-
+        }
 
 
         for (int k=0; k < alleleFrequencyPosteriors.length; k++) {
-            log10AlleleFrequencyPosteriors[k] = Math.log10(alleleFrequencyPosteriors[k]);
+            if (alleleFrequencyPosteriors[k] > 1-EPS)
+                log10AlleleFrequencyPosteriors[k] = -EPS;
+            else if (alleleFrequencyPosteriors[k] < EPS)
+                log10AlleleFrequencyPosteriors[k] = LOGEPS;
+            else
+                log10AlleleFrequencyPosteriors[k] = Math.log10(alleleFrequencyPosteriors[k]);
         }
     }
 
@@ -131,6 +138,24 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
     }
 
+    /**
+     * Can be overridden by concrete subclasses
+     * @param contexts             alignment contexts
+     * @param GLs                  genotype likelihoods
+     * @param log10AlleleFrequencyPosteriors    allele frequency results
+     * @param AFofMaxLikelihood    allele frequency of max likelihood
+     *
+     * @return calls
+     */
+    public Map<String, Genotype> assignGenotypes(Map<String, StratifiedAlignmentContext> contexts,
+                                                 Map<String, BiallelicGenotypeLikelihoods> GLs,
+                                                 double[] log10AlleleFrequencyPosteriors,
+                                                 int AFofMaxLikelihood) {
+
+        // overriding implementation in AlleleFrequencyCalculationModel to avoid filling out AF matrix which is not used.
+        return generateCalls(contexts, GLs, AFofMaxLikelihood);
+    }
+
     protected Map<String, Genotype> generateCalls(Map<String, StratifiedAlignmentContext> contexts,
                                                   Map<String, BiallelicGenotypeLikelihoods> GLs,
                                                   int bestAFguess) {
@@ -242,4 +267,4 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         return calls;
     }
 
-}
\ No newline at end of file
+}