diff --git a/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
index 15f1f4846..43dc6a6de 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
@@ -37,6 +37,11 @@ import net.sf.samtools.SAMRecord;
 public class BadMateFilter implements SamRecordFilter {
 
     public boolean filterOut(final SAMRecord rec) {
-        return (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
+        return hasBadMate(rec);
     }
+
+    public static boolean hasBadMate(final SAMRecord rec) {
+        return (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && !rec.getReferenceIndex().equals(rec.getMateReferenceIndex()));
+    }
+
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index 3f5190bdf..43afe2db3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -22,8 +22,8 @@ public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation
             return null;
 
         int depth = 0;
-        for ( String sample : stratifiedContexts.keySet() )
-            depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() )
+            depth += sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();
         Map<String, Object> map = new HashMap<String, Object>();
         map.put(getKeyNames().get(0), String.format("%d", depth));
         return map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index 719ab8fe0..763401fac 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -237,7 +237,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
         public String toString() { return new String(this.bases); }
     }
 
-    private class BaseQual extends Pair<Byte, Byte> {
+    private static class BaseQual extends Pair<Byte, Byte> {
         public BaseQual(byte base, byte qual) {
             super(base, qual);
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index fcd87c3ec..f10b2f70b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -25,9 +25,9 @@ public class LowMQ implements InfoFieldAnnotation {
         double mq0 = 0;
 		double mq10 = 0;
 		double total = 0;
-        for ( String sample : stratifiedContexts.keySet() ) 
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() )
 		{
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
+            ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             for (PileupElement p : pileup ) 
 			{
                 if ( p.getMappingQual() == 0 )  { mq0 += 1; }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index a7ee2ae2b..555d8823b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -24,8 +24,8 @@ public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotati
             return null;
 
         int mq0 = 0;
-        for ( String sample : stratifiedContexts.keySet() ) {
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             for (PileupElement p : pileup ) {
                 if ( p.getMappingQual() == 0 )
                     mq0++;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index bf3c98116..433713faa 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -23,8 +23,8 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
             return null;
 
         ArrayList<Integer> qualities = new ArrayList<Integer>();
-        for ( String sample : stratifiedContexts.keySet() ) {
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             for (PileupElement p : pileup )
                 qualities.add(p.getRead().getMappingQuality());
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 49c5bb533..e40f7df8e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -24,8 +24,8 @@ public class SpanningDeletions implements InfoFieldAnnotation, StandardAnnotatio
 
         int deletions = 0;
         int depth = 0;
-        for ( String sample : stratifiedContexts.keySet() ) {
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             deletions += pileup.getNumberOfDeletions();
             depth += pileup.size();
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
index 7a9b609fc..53d3e6607 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -69,15 +69,14 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         // use flat priors for GLs
         DiploidGenotypePriors priors = new DiploidGenotypePriors();
 
-        for ( String sample : contexts.keySet() ) {
-            StratifiedAlignmentContext context = contexts.get(sample);
-            ReadBackedPileup pileup = context.getContext(contextType).getBasePileup();
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : contexts.entrySet() ) {
+            ReadBackedPileup pileup = sample.getValue().getContext(contextType).getBasePileup();
 
             // create the GenotypeLikelihoods object
             GenotypeLikelihoods GL = new GenotypeLikelihoods(UAC.baseModel, priors, UAC.defaultPlatform);
 
             GL.add(pileup, true, UAC.CAP_BASE_QUALITY);
-            GLs.put(sample, GL);
+            GLs.put(sample.getKey(), GL);
 
             double[] posteriors = GL.getPosteriors();
 
@@ -87,7 +86,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
                 if ( alt != ref ) {
                     DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(ref, alt);
                     DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
-                    AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample);
+                    AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample.getKey());
                 }
             }
         }
@@ -171,7 +170,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
     }
 
 
-    protected class AlleleFrequencyMatrix {
+    protected static class AlleleFrequencyMatrix {
 
         private double[][] matrix;    // allele frequency matrix
         private int[] indexes;        // matrix to maintain which genotype is active
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
index cce076d92..9c6bf62a9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
@@ -57,7 +57,7 @@ public class DiploidGenotypePriors {
     private double[] priors = null;
 
     // todo -- fix me when this issue is resolved
-    public static boolean RequirePriorSumToOne = false;
+    public static final boolean requirePriorSumToOne = false;
 
     /**
      * Create a new DiploidGenotypePriors object with flat priors for each diploid genotype
@@ -124,7 +124,7 @@ public class DiploidGenotypePriors {
 
    public boolean validate(boolean throwException) {
         try {
-            if ( RequirePriorSumToOne && MathUtils.compareDoubles(MathUtils.sumLog10(priors), 1.0) != 0 ) {
+            if ( requirePriorSumToOne && MathUtils.compareDoubles(MathUtils.sumLog10(priors), 1.0) != 0 ) {
                 throw new IllegalStateException(String.format("Priors don't sum to 1: sum=%f %s", MathUtils.sumLog10(priors), Arrays.toString(priors)));
             }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
index cc4773688..b0d74695b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
@@ -101,7 +101,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
 
         double logP = log10pTrueGivenMiscall.get(pl)[i][j];
         if ( logP == 0.0 )
-            throw new RuntimeException(String.format("Bad miscall base request miscalled=%c true=%b", miscalledBase, trueBase));
+            throw new RuntimeException(String.format("Bad miscall base request miscalled=%c true=%c", miscalledBase, trueBase));
         else
             return logP;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilitiesFactory.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilitiesFactory.java
index 5b427c423..3031d69a5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilitiesFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilitiesFactory.java
@@ -6,11 +6,7 @@ public class FourBaseProbabilitiesFactory {
     //private FourBaseProbabilitiesFactory() {} // cannot be instantiated
 
     public static BaseMismatchModel getBaseMismatchModel(final String name) {
-        BaseMismatchModel m = valueOf(name);
-        if ( m == null )
-            throw new RuntimeException("Unexpected BaseMismatchModel " + name);
-        else
-            return m;
+        return valueOf(name);
     }
 
     public static BaseMismatchModel getBaseMismatchModel(final FourBaseProbabilities m) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
index d66d45266..cbc6950e4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
@@ -37,11 +37,7 @@ public class GenotypeCalculationModelFactory {
     //private GenotypeCalculationModelFactory() {} // cannot be instantiated
 
     public static GenotypeCalculationModel.Model getGenotypeCalculationModel(final String name) {
-        GenotypeCalculationModel.Model m = valueOf(name);
-        if ( m == null )
-            throw new RuntimeException("Unexpected GenotypeCalculationModel " + name);
-        else
-            return m;
+        return valueOf(name);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index f9b280ba8..04cec3f8a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -499,7 +499,7 @@ public class GenotypeLikelihoods implements Cloneable {
     //
     // Constant static data
     //
-    protected final static double[] zeros = new double[DiploidGenotype.values().length];
+    final static double[] zeros = new double[DiploidGenotype.values().length];
 
     static {
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index e44bfea8b..101cd1ea9 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -13,8 +13,8 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
 
     // for use in optimizing the P(D|AF) calculations:
     // how much off from the max likelihoods do we need to be before we can quit calculating?
-    protected static final Double LOG10_OPTIMIZATION_EPSILON = 8.0;
-    protected static final Double VALUE_NOT_CALCULATED = -1.0 * Double.MAX_VALUE;
+    protected static final double LOG10_OPTIMIZATION_EPSILON = 8.0;
+    protected static final double VALUE_NOT_CALCULATED = -1.0 * Double.MAX_VALUE;
     private int minAlleleFrequencyToTest;
 
     // because the null allele frequencies are constant for a given N,
@@ -107,11 +107,9 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
     protected void initializeBestAlternateAllele(byte ref, Map<String, StratifiedAlignmentContext> contexts) {
         int[] qualCounts = new int[4];
 
-        for ( String sample : contexts.keySet() ) {
-            AlignmentContext context = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
-
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : contexts.entrySet() ) {
             // calculate the sum of quality scores for each base
-            ReadBackedPileup pileup = context.getBasePileup();
+            ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             for ( PileupElement p : pileup ) {
                 // ignore deletions
                 if ( p.isDeletion() )
@@ -409,7 +407,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
             strandScore *= 10.0;
             //logger.debug(String.format("SLOD=%f", strandScore));
 
-            attributes.put("SB", new Double(strandScore));
+            attributes.put("SB", Double.valueOf(strandScore));
         }
 
         VariantContext vc = new VariantContext("UG_SNP_call", loc, alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence) ? null : filter, attributes);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
index 35db3ea45..4c61f38c3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
@@ -92,8 +92,8 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
     protected void initializeAlleles(byte[] ref, Map<String, StratifiedAlignmentContext> contexts) {
 
 
-        for ( String sample : contexts.keySet() ) {
-            AlignmentContext context = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : contexts.entrySet() ) {
+            AlignmentContext context = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
 
             totalCoverage += context.size();
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 3a25f3678..85e82bf5c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -82,7 +82,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     /**
      * Inner class for collecting output statistics from the UG
      */
-    public class UGStatistics {
+    public static class UGStatistics {
         /** The total number of passes examined -- i.e., the number of map calls */
         long nBasesVisited = 0;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index b6b1202a0..2f1c84194 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@@ -155,7 +156,7 @@ public class UnifiedGenotyperEngine {
             return null;
 
         VariantCallContext call;
-        BadlyMatedReadPileupFilter badlyMatedReadPileupFilter = new BadlyMatedReadPileupFilter(refContext);
+        BadReadPileupFilter badReadPileupFilter = new BadReadPileupFilter(refContext);
 
         if ( rawContext.hasExtendedEventPileup() ) {
 
@@ -165,7 +166,7 @@ public class UnifiedGenotyperEngine {
             ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE);
 
             // filter the context based on bad mates and mismatch rate
-            pileup = pileup.getFilteredPileup(badlyMatedReadPileupFilter);
+            pileup = pileup.getFilteredPileup(badReadPileupFilter);
 
             // don't call when there is no coverage
             if ( pileup.size() == 0 && !UAC.ALL_BASES_MODE )
@@ -186,7 +187,7 @@ public class UnifiedGenotyperEngine {
             ReadBackedPileup pileup = rawPileup.getBaseAndMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE, UAC.MIN_MAPPING_QUALTY_SCORE);
 
             // filter the context based on bad mates and mismatch rate
-            pileup = pileup.getFilteredPileup(badlyMatedReadPileupFilter);
+            pileup = pileup.getFilteredPileup(badReadPileupFilter);
 
             // don't call when there is no coverage
             if ( pileup.size() == 0 && !UAC.ALL_BASES_MODE )
@@ -227,16 +228,13 @@ public class UnifiedGenotyperEngine {
     /**
      * Filters low quality reads out of the pileup.
      */
-    private class BadlyMatedReadPileupFilter implements PileupElementFilter {
+    private class BadReadPileupFilter implements PileupElementFilter {
         private ReferenceContext refContext;
 
-        public BadlyMatedReadPileupFilter(ReferenceContext refContext) { this.refContext = refContext; }
+        public BadReadPileupFilter(ReferenceContext refContext) { this.refContext = refContext; }
 
         public boolean allow(PileupElement pileupElement) {
-            return  ((UAC.USE_BADLY_MATED_READS ||
-                      !pileupElement.getRead().getReadPairedFlag() ||
-                      pileupElement.getRead().getMateUnmappedFlag() ||
-                      pileupElement.getRead().getMateReferenceIndex() == pileupElement.getRead().getReferenceIndex()) &&
+            return  ((UAC.USE_BADLY_MATED_READS || !BadMateFilter.hasBadMate(pileupElement.getRead())) &&
                      AlignmentUtils.mismatchesInRefWindow(pileupElement, refContext, true) <= UAC.MAX_MISMATCHES );
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index e52fd81c4..0f8223bc4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@@ -298,7 +299,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 read.getReadFailsVendorQualityCheckFlag() ||
                 read.getMappingQuality() == 0 ||
                 read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
-                (!REALIGN_BADLY_MATED_READS && read.getReadPairedFlag() && !read.getMateUnmappedFlag() && read.getMateReferenceIndex() != read.getReferenceIndex());
+                (!REALIGN_BADLY_MATED_READS && BadMateFilter.hasBadMate(read));
     }
 
     private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
@@ -510,7 +511,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         statsOutput.write(Double.toString(improvement));
                         statsOutput.write("\n");
                         statsOutput.flush();
-                    } catch (Exception e) {}
+                    } catch (Exception e) {
+                        throw new StingException(e.getMessage());
+                    }
                 }
             } else {
                 //logger.debug("CLEAN: " + bestConsensus.cigar + " " + bestConsensus.str.toString() + " " + bestConsensus.cigar.numCigarElements() );
@@ -535,7 +538,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                     try {
                         indelOutput.write(str.toString());
                         indelOutput.flush();
-                    } catch (Exception e) {}
+                    } catch (Exception e) {
+                        throw new StingException(e.getMessage());
+                    }
                 }
                 if ( statsOutput != null ) {
                     try {
@@ -547,7 +552,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         statsOutput.write(Double.toString(improvement));
                         statsOutput.write("\n");
                         statsOutput.flush();
-                    } catch (Exception e) {}
+                    } catch (Exception e) {
+                        throw new StingException(e.getMessage());
+                    }
                 }
 
                 // finish cleaning the appropriate reads
@@ -571,7 +578,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 statsOutput.write(String.format("%s\tFAIL\t%.1f%n",
                         readsToClean.getLocation().toString(), improvement));
                 statsOutput.flush();
-            } catch (Exception e) {}
+            } catch (Exception e) {
+                throw new StingException(e.getMessage());
+            }
         }
     }
 
@@ -999,7 +1008,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             try {
                 snpsOutput.write(sb.toString());
                 snpsOutput.flush();
-            } catch (Exception e) {}
+            } catch (Exception e) {
+                throw new StingException(e.getMessage());                
+            }
         }
         return reduces;
     }
@@ -1200,7 +1211,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         }
     }
 
-    private class Consensus {
+    private static class Consensus {
         public final byte[] str;
         public final ArrayList<Pair<Integer, Integer>> readIndexes;
         public final int positionOnReference;
@@ -1230,7 +1241,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         }
     }
 
-    private class ReadBin {
+    private static class ReadBin {
 
         private final ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
         private byte[] reference = null;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 773965643..5bbed58c7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -91,7 +91,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
         long furthestStopPos = -1;
 
         // look for insertions in the extended context (we'll get deletions from the normal context)
-        if ( context != null && context.hasExtendedEventPileup() ) {
+        if ( context.hasExtendedEventPileup() ) {
             ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup();
             if ( pileup.getNumberOfInsertions() > 0 ) {
                 hasIndel = hasInsertion = true;
@@ -119,6 +119,8 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
                         if ( vc.isInsertion() )
                             hasInsertion = true;
                         break;
+                    default:
+                        break;
                 }
                 if ( hasIndel )
                     furthestStopPos = vc.getLocation().getStop();
@@ -132,12 +134,11 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
             int mismatchQualities = 0, totalQualities = 0;
             byte refBase = ref.getBase();
             for (PileupElement p : pileup ) {
-                SAMRecord read = p.getRead();
-                if ( !REALIGN_BADLY_MATED_READS && read.getReadPairedFlag() && !read.getMateUnmappedFlag() && read.getMateReferenceIndex() != read.getReferenceIndex() )
+                if ( !REALIGN_BADLY_MATED_READS && BadMateFilter.hasBadMate(p.getRead()) )
                     continue;
 
                 // check the ends of the reads to see how far they extend
-                furthestStopPos = Math.max(furthestStopPos, read.getAlignmentEnd());
+                furthestStopPos = Math.max(furthestStopPos, p.getRead().getAlignmentEnd());
 
                 // is it a deletion? (sanity check in case extended event missed it)
                 if ( p.isDeletion() ) {