diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
new file mode 100755
index 000000000..59357e1c4
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
@@ -0,0 +1,197 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.downsampling;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.pileup.*;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.io.PrintStream;
+import java.util.*;
+
+public class AlleleBiasedDownsamplingUtils {
+
+    /**
+     * Computes an allele biased version of the given pileup
+     *
+     * @param pileup                    the original pileup
+     * @param downsamplingFraction      the fraction of total reads to remove per allele
+     * @param log                       logging output
+     * @return allele biased pileup
+     */
+    public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
+        // special case removal of all or no reads
+        if ( downsamplingFraction <= 0.0 )
+            return pileup;
+        if ( downsamplingFraction >= 1.0 )
+            return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
+
+        final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
+        for ( int i = 0; i < 4; i++ )
+            alleleStratifiedElements[i] = new ArrayList<PileupElement>();
+
+        // start by stratifying the reads by the alleles they represent at this position
+        for( final PileupElement pe : pileup ) {
+            // abort if we have a reduced read - we do not want to remove it!
+            if ( pe.getRead().isReducedRead() )
+                return pileup;
+
+            final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
+            if ( baseIndex != -1 )
+                alleleStratifiedElements[baseIndex].add(pe);
+        }
+
+        // Down-sample *each* allele by the contamination fraction applied to the entire pileup.
+        // Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later.
+        int numReadsToRemove = (int)(pileup.getNumberOfElements() * downsamplingFraction); // floor
+        final TreeSet<PileupElement> elementsToKeep = new TreeSet<PileupElement>(new Comparator<PileupElement>() {
+            @Override
+            public int compare(PileupElement element1, PileupElement element2) {
+                final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
+                return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
+            }
+        });
+
+        for ( int i = 0; i < 4; i++ ) {
+            final ArrayList<PileupElement> alleleList = alleleStratifiedElements[i];
+            if ( alleleList.size() <= numReadsToRemove )
+                logAllElements(alleleList, log);
+            else
+                elementsToKeep.addAll(downsampleElements(alleleList, numReadsToRemove, log));
+        }
+
+        // clean up pointers so memory can be garbage collected if needed
+        for ( int i = 0; i < 4; i++ )
+            alleleStratifiedElements[i].clear();
+
+        return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>(elementsToKeep));
+    }
+
+    /**
+     * Performs allele biased down-sampling on a pileup and computes the list of elements to keep
+     *
+     * @param elements                  original list of records
+     * @param numElementsToRemove       the number of records to remove
+     * @param log                       logging output
+     * @return the list of pileup elements TO KEEP
+     */
+    private static List<PileupElement> downsampleElements(final ArrayList<PileupElement> elements, final int numElementsToRemove, final PrintStream log) {
+        final int pileupSize = elements.size();
+        final BitSet itemsToRemove = new BitSet(pileupSize);
+        for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
+            itemsToRemove.set(selectedIndex);
+        }
+
+        ArrayList<PileupElement> elementsToKeep = new ArrayList<PileupElement>(pileupSize - numElementsToRemove);
+        for ( int i = 0; i < pileupSize; i++ ) {
+            if ( itemsToRemove.get(i) )
+                logRead(elements.get(i).getRead(), log);
+            else
+                elementsToKeep.add(elements.get(i));
+        }
+
+        return elementsToKeep;
+    }
+
+    /**
+     * Computes reads to remove based on an allele biased down-sampling
+     *
+     * @param alleleReadMap             original list of records per allele
+     * @param downsamplingFraction      the fraction of total reads to remove per allele
+     * @param log                       logging output
+     * @return list of reads TO REMOVE from allele biased down-sampling
+     */
+    public static List<GATKSAMRecord> selectAlleleBiasedReads(final Map<Allele, List<GATKSAMRecord>> alleleReadMap, final double downsamplingFraction, final PrintStream log) {
+        int totalReads = 0;
+        for ( final List<GATKSAMRecord> reads : alleleReadMap.values() )
+            totalReads += reads.size();
+
+        // Down-sample *each* allele by the contamination fraction applied to the entire pileup.
+        int numReadsToRemove = (int)(totalReads * downsamplingFraction);
+        final List<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>(numReadsToRemove * alleleReadMap.size());
+        for ( final List<GATKSAMRecord> reads : alleleReadMap.values() ) {
+            if ( reads.size() <= numReadsToRemove ) {
+                readsToRemove.addAll(reads);
+                logAllReads(reads, log);
+            } else {
+                readsToRemove.addAll(downsampleReads(reads, numReadsToRemove, log));
+            }
+        }
+
+        return readsToRemove;
+    }
+
+    /**
+     * Performs allele biased down-sampling on a pileup and computes the list of elements to remove
+     *
+     * @param reads                     original list of records
+     * @param numElementsToRemove       the number of records to remove
+     * @param log                       logging output
+     * @return the list of pileup elements TO REMOVE
+     */
+    private static List<GATKSAMRecord> downsampleReads(final List<GATKSAMRecord> reads, final int numElementsToRemove, final PrintStream log) {
+        final int pileupSize = reads.size();
+        final BitSet itemsToRemove = new BitSet(pileupSize);
+        for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
+            itemsToRemove.set(selectedIndex);
+        }
+
+        ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>(pileupSize - numElementsToRemove);
+        for ( int i = 0; i < pileupSize; i++ ) {
+            if ( itemsToRemove.get(i) ) {
+                final GATKSAMRecord read = reads.get(i);
+                readsToRemove.add(read);
+                logRead(read, log);
+            }
+        }
+
+        return readsToRemove;
+    }
+
+    private static void logAllElements(final List<PileupElement> elements, final PrintStream log) {
+        if ( log != null ) {
+            for ( final PileupElement p : elements )
+                logRead(p.getRead(), log);
+        }
+    }
+
+    private static void logAllReads(final List<GATKSAMRecord> reads, final PrintStream log) {
+        if ( log != null ) {
+            for ( final GATKSAMRecord read : reads )
+                logRead(read, log);
+        }
+    }
+
+    private static void logRead(final SAMRecord read, final PrintStream log) {
+        if ( log != null ) {
+            final SAMReadGroupRecord readGroup = read.getReadGroup();
+            log.println(String.format("%s\t%s\t%s\t%s", read.getReadName(), readGroup.getSample(), readGroup.getLibrary(), readGroup.getPlatformUnit()));
+        }
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
index b89f68e24..d0bcd0eb3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
@@ -28,89 +28,32 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
 import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
-import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.recalibration.EventType;
 import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
-import org.broadinstitute.sting.utils.recalibration.RecalDatum;
 import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.threading.ThreadLocalArray;
 
 public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine implements ProtectedPackageSource {
 
-    // optimizations: don't reallocate an array each time
-    private byte[] tempQualArray;
-    private boolean[] tempErrorArray;
-    private double[] tempFractionalErrorArray;
+    // optimization: only allocate temp arrays once per thread
+    private final ThreadLocal<byte[]> threadLocalTempQualArray = new ThreadLocalArray<byte[]>(EventType.values().length, byte.class);
+    private final ThreadLocal<double[]> threadLocalTempFractionalErrorArray = new ThreadLocalArray<double[]>(EventType.values().length, double.class);
 
     public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
         super.initialize(covariates, recalibrationTables);
-        tempQualArray = new byte[EventType.values().length];
-        tempErrorArray = new boolean[EventType.values().length];
-        tempFractionalErrorArray = new double[EventType.values().length];
-    }
-
-    /**
-     * Loop through the list of requested covariates and pick out the value from the read, offset, and reference
-     * Using the list of covariate values as a key, pick out the RecalDatum and increment,
-     * adding one to the number of observations and potentially one to the number of mismatches for all three
-     * categories (mismatches, insertions and deletions).
-     *
-     * @param pileupElement The pileup element to update
-     * @param refBase       The reference base at this locus
-     */
-    @Override
-    public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {
-        final int offset = pileupElement.getOffset();
-        final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead());
-
-        tempQualArray[EventType.BASE_SUBSTITUTION.index] = pileupElement.getQual();
-        tempErrorArray[EventType.BASE_SUBSTITUTION.index] = !BaseUtils.basesAreEqual(pileupElement.getBase(), refBase);
-        tempQualArray[EventType.BASE_INSERTION.index] = pileupElement.getBaseInsertionQual();
-        tempErrorArray[EventType.BASE_INSERTION.index] = (pileupElement.getRead().getReadNegativeStrandFlag()) ? pileupElement.isAfterInsertion() : pileupElement.isBeforeInsertion();
-        tempQualArray[EventType.BASE_DELETION.index] = pileupElement.getBaseDeletionQual();
-        tempErrorArray[EventType.BASE_DELETION.index] = (pileupElement.getRead().getReadNegativeStrandFlag()) ? pileupElement.isAfterDeletedBase() : pileupElement.isBeforeDeletedBase();
-
-        for (final EventType eventType : EventType.values()) {
-            final int[] keys = readCovariates.getKeySet(offset, eventType);
-            final int eventIndex = eventType.index;
-            final byte qual = tempQualArray[eventIndex];
-            final boolean isError = tempErrorArray[eventIndex];
-
-            final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getReadGroupTable();
-            final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
-            final RecalDatum rgThisDatum = createDatumObject(qual, isError);
-            if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
-                rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
-            else
-                rgPreviousDatum.combine(rgThisDatum);
-
-            final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getQualityScoreTable();
-            final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
-            if (qualPreviousDatum == null)
-                qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
-            else
-                qualPreviousDatum.increment(isError);
-
-            for (int i = 2; i < covariates.length; i++) {
-                if (keys[i] < 0)
-                    continue;
-                final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
-                final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
-                if (covPreviousDatum == null)
-                    covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
-                else
-                    covPreviousDatum.increment(isError);
-            }
-        }
     }
 
     @Override
-    public synchronized void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
+    public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
         for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
             if( !skip[offset] ) {
                 final ReadCovariates readCovariates = covariateKeySetFrom(read);
 
+                byte[] tempQualArray = threadLocalTempQualArray.get();
+                double[] tempFractionalErrorArray = threadLocalTempFractionalErrorArray.get();
+
                 tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset];
                 tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset];
                 tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset];
@@ -124,30 +67,15 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp
                     final byte qual = tempQualArray[eventIndex];
                     final double isError = tempFractionalErrorArray[eventIndex];
 
-                    final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getReadGroupTable();
-                    final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
-                    final RecalDatum rgThisDatum = createDatumObject(qual, isError);
-                    if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
-                        rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
-                    else
-                        rgPreviousDatum.combine(rgThisDatum);
+                    combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex);
 
-                    final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getQualityScoreTable();
-                    final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
-                    if (qualPreviousDatum == null)
-                        qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
-                    else
-                        qualPreviousDatum.increment(1.0, isError);
+                    incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex);
 
                     for (int i = 2; i < covariates.length; i++) {
                         if (keys[i] < 0)
                             continue;
-                        final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
-                        final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
-                        if (covPreviousDatum == null)
-                            covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
-                        else
-                            covPreviousDatum.increment(1.0, isError);
+
+                        incrementDatumOrPutIfNecessary(recalibrationTables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
                     }
                 }
             }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
index 8042c15d8..fc6d23382 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import com.google.java.contract.Requires;
-import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -60,7 +60,7 @@ public class ErrorModel  {
 
         boolean hasCalledAlleles = false;
 
-        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
+        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
         if (refSampleVC != null) {
 
             for (Allele allele : refSampleVC.getAlleles()) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
index 2522fc16e..f6ad445c7 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
@@ -195,7 +195,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
                                          final List<Allele> allAllelesToUse,
                                          final boolean useBAQedPileup,
                                          final GenomeLocParser locParser,
-                                         final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                         final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
 
         HashMap<String, ErrorModel> perLaneErrorModels = getPerLaneErrorModels(tracker, ref, contexts);
         if (perLaneErrorModels == null && UAC.referenceSampleName != null)
@@ -231,7 +231,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
             ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
             }
 
             // create the GenotypeLikelihoods object
@@ -333,7 +333,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
                                                                                final boolean useBQAedPileup,
                                                                                final ReferenceContext ref,
                                                                                final boolean ignoreLaneInformation,
-                                                                               final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap);
+                                                                               final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap);
 
     protected abstract List<Allele> getInitialAllelesToUse(final RefMetaDataTracker tracker,
                                                            final ReferenceContext ref,
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
index afbd49a08..4bcaa5ff9 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
@@ -27,7 +27,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
     double[][] readHaplotypeLikelihoods;
 
     final byte refBase;
-    final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;
+    final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;
 
     public GeneralPloidyIndelGenotypeLikelihoods(final List<Allele> alleles,
                                                  final double[] logLikelihoods,
@@ -37,7 +37,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
                                                  final PairHMMIndelErrorModel pairModel,
                                                  final LinkedHashMap<Allele, Haplotype> haplotypeMap,
                                                  final ReferenceContext referenceContext,
-                                                 final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) {
+                                                 final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) {
         super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation);
         this.pairModel = pairModel;
         this.haplotypeMap = haplotypeMap;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
index f09a1ea3e..eb4cf1839 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
@@ -74,7 +74,7 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener
                                                                                final boolean useBQAedPileup,
                                                                                final ReferenceContext ref,
                                                                                final boolean ignoreLaneInformation,
-                                                                               final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
+                                                                               final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
         return new GeneralPloidyIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref, perReadAlleleLikelihoodMap);
     }
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
index 4376ec601..9f2fdc096 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
@@ -50,7 +50,7 @@ public class GeneralPloidySNPGenotypeLikelihoodsCalculationModel extends General
                                                                                final boolean useBQAedPileup,
                                                                                final ReferenceContext ref,
                                                                                final boolean ignoreLaneInformation,
-                                                                               final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
+                                                                               final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
         return new GeneralPloidySNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO);
     }
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 8738def50..d91df82e2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -217,7 +217,7 @@ public class GenotypingEngine {
         }
 
         cleanUpSymbolicUnassembledEvents( haplotypes );
-        if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 3 ) { // if not in GGA mode and have at least 3 samples try to create MNP and complex events by looking at LD structure
+        if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
             mergeConsecutiveEventsBasedOnLD( haplotypes, startPosKeySet, ref, refLoc );
         }
         if( !activeAllelesToGenotype.isEmpty() ) { // we are in GGA mode!
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index a08614deb..5aba23faa 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -51,6 +51,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
 import org.broadinstitute.sting.utils.fragments.FragmentUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -424,7 +425,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
                   : genotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents( UG_engine, bestHaplotypes, fullReferenceWithPadding, getPaddedLoc(activeRegion), activeRegion.getLocation(), getToolkit().getGenomeLocParser(), activeAllelesToGenotype ) ) ) {
             if( DEBUG ) { System.out.println(callResult.getFirst().toStringWithoutGenotypes()); }
 
-            final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = LikelihoodCalculationEngine.partitionReadsBasedOnLikelihoods( getToolkit().getGenomeLocParser(), perSampleReadList, perSampleFilteredReadList, callResult );
+            final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = LikelihoodCalculationEngine.partitionReadsBasedOnLikelihoods( getToolkit().getGenomeLocParser(), perSampleReadList, perSampleFilteredReadList, callResult, UG_engine.getUAC().CONTAMINATION_FRACTION, UG_engine.getUAC().contaminationLog );
             final VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, callResult.getFirst());
             final Map<String, Object> myAttributes = new LinkedHashMap<String, Object>(annotatedCall.getAttributes());
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 62554c4ab..a0924623b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.io.PrintStream;
 import java.util.*;
 
 public class LikelihoodCalculationEngine {
@@ -139,7 +140,7 @@ public class LikelihoodCalculationEngine {
     }
 
     private static int computeFirstDifferingPosition( final byte[] b1, final byte[] b2 ) {
-        for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ){
+        for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ) {
             if( b1[iii] != b2[iii] ) {
                 return iii;
             }
@@ -346,11 +347,13 @@ public class LikelihoodCalculationEngine {
     public static Map<String, PerReadAlleleLikelihoodMap> partitionReadsBasedOnLikelihoods( final GenomeLocParser parser,
                                                                                             final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList,
                                                                                             final HashMap<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList,
-                                                                                            final Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>> call) {
+                                                                                            final Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>> call,
+                                                                                            final double downsamplingFraction,
+                                                                                            final PrintStream downsamplingLog ) {
         final Map<String, PerReadAlleleLikelihoodMap> returnMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
         final GenomeLoc callLoc = parser.createGenomeLoc(call.getFirst());
         for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
-            final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
+            final PerReadAlleleLikelihoodMap likelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
 
             final ArrayList<GATKSAMRecord> readsForThisSample = sample.getValue();
             for( int iii = 0; iii < readsForThisSample.size(); iii++ ) {
@@ -370,6 +373,9 @@ public class LikelihoodCalculationEngine {
                 }
             }
 
+            // down-sample before adding filtered reads
+            likelihoodMap.performPerAlleleDownsampling(downsamplingFraction, downsamplingLog);
+
             // add all filtered reads to the NO_CALL list because they weren't given any likelihoods
             for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) {
                 // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
new file mode 100644
index 000000000..77a7c3bd9
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+package org.broadinstitute.sting.utils.genotyper;
+
+
+import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
+import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.io.PrintStream;
+import java.util.*;
+
+public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLikelihoodMap implements ProtectedPackageSource {
+
+    public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
+        return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log);
+    }
+
+    public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {
+        // special case removal of all or no reads
+        if ( downsamplingFraction <= 0.0 )
+            return;
+        if ( downsamplingFraction >= 1.0 ) {
+            likelihoodReadMap.clear();
+            return;
+        }
+
+        // start by stratifying the reads by the alleles they represent at this position
+        final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
+        for ( Allele allele : alleles )
+            alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
+
+        for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
+            // do not remove reduced reads!
+            if ( !entry.getKey().isReducedRead() ) {
+                final Allele bestAllele = getMostLikelyAllele(entry.getValue());
+                if ( bestAllele != Allele.NO_CALL )
+                    alleleReadMap.get(bestAllele).add(entry.getKey());
+            }
+        }
+
+        // compute the reads to remove and actually remove them
+        final List<GATKSAMRecord> readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log);
+        for ( final GATKSAMRecord read : readsToRemove )
+            likelihoodReadMap.remove(read);
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
index 26ee78484..b839382dc 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
@@ -5,7 +5,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 
 /**
  * @author ebanks
@@ -49,21 +51,21 @@ public class BQSRIntegrationTest extends WalkerTest {
         String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
         String HiSeqInterval = "chr1:10,000,000-10,100,000";
         return new Object[][]{
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "55a46d8f5d2f9acfa2d7659e18b6df43")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "8e930f56a8905a5999af7d6ba8a92f91")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "8e87bee4bd6531b405082c4da785f1f5")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "b309a5f57b861d7f31cb76cdac4ff8a7")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "4c75d47ed2cf93b499be8fbb29b24dfd")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "43b06e5568a89e4ce1dd9146ce580c89")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "25f4f48dba27475b0cd7c06ef0239aba")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "dfcba9acc32b4a1dfeceea135b48615a")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "e8077b721f2e6f51c1945b6f6236835c")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "fbdc8d0fd312e3a7f49063c580cf5d92")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "4f47415628201a4f3c33e48ec066677b")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "1e89d2b88f4218363b9322b38e9536f2")},
-                {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "a7beb0b16756257a274eecf73474ed90")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "dfcba9acc32b4a1dfeceea135b48615a")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "2082c70e08f1c14290c3812021832f83")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "387b41dc2221a1a4a782958944662b25")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "b5e26902e76abbd59f94f65c70d18165")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "a8a9c3f83269911cb61c5fe8fb98dc4a")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "f43a0473101c63ae93444c300d843e81")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "9e05e63339d4716584bfc717cab6bd0f")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "1cf9b9c9c64617dc0f3d2f203f918dbe")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "aa1949a77bc3066fee551a217c970c0d")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "f70d8b5358bc2f76696f14b7a807ede0")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "4c0f63e06830681560a1e9f9aad9fe98")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "be2812cd3dae3c326cf35ae3f1c8ad9e")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "03c29a0c1d21f72b12daf51cec111599")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "7080b2cad02ec6e67ebc766b2dccebf8")},
+                {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "30e76055c16843b6e33e5b9bd8ced57c")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "f70d8b5358bc2f76696f14b7a807ede0")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5e657fd6a44dcdc7674b6e5a2de5dc83")},
         };
     }
 
@@ -73,11 +75,6 @@ public class BQSRIntegrationTest extends WalkerTest {
                 params.getCommandLine(),
                 Arrays.asList(params.md5));
         executeTest("testBQSR-"+params.args, spec).getFirst();
-
-        WalkerTestSpec specNT2 = new WalkerTestSpec(
-                params.getCommandLine() + " -nt 2",
-                Arrays.asList(params.md5));
-        executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst();
     }
 
     @Test
@@ -123,20 +120,26 @@ public class BQSRIntegrationTest extends WalkerTest {
 
     @DataProvider(name = "PRTest")
     public Object[][] createPRTestData() {
-        return new Object[][]{
-                {new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")},
-                {new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")},
-                {new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")},
-                {new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")}
-        };
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        tests.add(new Object[]{1, new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")});
+        tests.add(new Object[]{1, new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")});
+        tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")});
+
+        for ( final int nct : Arrays.asList(1, 2, 4) ) {
+            tests.add(new Object[]{nct, new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")});
+        }
+
+        return tests.toArray(new Object[][]{});
     }
 
     @Test(dataProvider = "PRTest")
-    public void testPR(PRTest params) {
+    public void testPR(final int nct, PRTest params) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T PrintReads" +
                         " -R " + hg18Reference +
                         " -I " + privateTestDir + "HiSeq.1mb.1RG.bam" +
+                        " -nct " + nct +
                         " -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" +
                         params.args +
                         " -o %s",
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
index ae3befe66..73bc8fba6 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
@@ -55,36 +55,36 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSNP_ACS_Pools() {
-        PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","ec19f0b7c7d57493cecfff988a4815c8");
+        PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","df0e67c975ef74d593f1c704daab1705");
     }
 
     @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","9ce24f4ff787aed9d3754519a60ef49f");
+        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","7e5b28c9e21cc7e45c58c41177d8a0fc");
     }
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","492c8ba9a80a902097ff15bbeb031592");
+        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","ae6c276cc46785a794acff6f7d10ecf7");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","848e1092b5cd57b0da5f1187e67134e7");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","481452ad7d6378cffb5cd834cc621d55");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","51a7b51d82a341adec0e6510f5dfadd8");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","812957e51277aca9925c1a7bb4d9a118");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
-         PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","0a8c3b06243040b743dd90d497bb3f83");
+         PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","dd568dc30be90135a3a8957a45a7321c");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "f8ea18ec6a717a77fdf8c5f2482d8d8d");
+        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "bf793c43b635a931207170be8035b288");
     }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 1d4fad19e..86f3748ce 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -21,17 +21,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "ee866a8694a6f6c77242041275350ab9");
+        HCTest(CEUTRIO_BAM, "", "aa1df35d6e64d7ca93feb4d2dd15dd0e");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "01367428c26d3eaf9297c58bf8677dd3");
+        HCTest(NA12878_BAM, "", "186c7f322978283c01249c6de2829215");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "53caa950535749f99d3c5b9bb61c7b60");
+        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "de9e78a52207fe62144dba5337965469");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(CEUTRIO_BAM, "", "30598abeeb0b0ae5816ffdbf0c4044fd");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "000dbb1b48f94d017cfec127c6cabe8f");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -53,7 +53,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleSymbolic() {
-        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "b4ea70a446e4782bd3700ca14dd726ff");
+        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "16013a9203367c3d1c4ce1dcdc81ef4a");
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -64,20 +64,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "2581e760279291a3901a506d060bfac8");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "b369c2a6cb5c99a424551b33bae16f3b");
     }
 
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c54c0c9411054bf629bfd98b616e53fc"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c306140ad28515ee06c603c225217939"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c642dcd93771f6f084d55de31f180d1b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b6c67ee8e99cc8f53a6587bb26028047"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -91,9 +91,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f"));
+                Arrays.asList("4beb9f87ab3f316a9384c3d0dca6ebe9"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
-
-
 }
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 54ade61f6..5d7eba16c 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -406,7 +406,7 @@ public abstract class ArgumentTypeDescriptor {
             else
                 throw new UserException.CommandLineException(
                         String.format("Failed to parse value %s for argument %s. Message: %s",
-                                value.asString(), fieldName, e.getMessage()));
+                                value, fieldName, e.getMessage()));
         }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 67e5ad95b..b7000e0ee 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -64,6 +64,7 @@ import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 
 import java.io.File;
 import java.util.*;
+import java.util.concurrent.TimeUnit;
 
 /**
  * A GenomeAnalysisEngine that runs a specified walker.
@@ -73,6 +74,7 @@ public class GenomeAnalysisEngine {
      * our log, which we want to capture anything from this class
      */
     private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
+    public static final long NO_RUNTIME_LIMIT = -1;
 
     /**
      * The GATK command-line argument parsing code.
@@ -1090,6 +1092,33 @@ public class GenomeAnalysisEngine {
     public String createApproximateCommandLineArgumentString(Object... argumentProviders) {
         return CommandLineUtils.createApproximateCommandLineArgumentString(parsingEngine,argumentProviders);
     }
-    
 
+    /**
+     * Does the current runtime in unit exceed the runtime limit, if one has been provided?
+     *
+     * @param runtime the runtime of this GATK instance in minutes
+     * @param unit the time unit of runtime
+     * @return false if not limit was requested or if runtime <= the limit, true otherwise
+     */
+    public boolean exceedsRuntimeLimit(final long runtime, final TimeUnit unit) {
+        if ( runtime < 0 ) throw new IllegalArgumentException("runtime must be >= 0 but got " + runtime);
+
+        if ( getArguments().maxRuntime == NO_RUNTIME_LIMIT )
+            return false;
+        else {
+            final long actualRuntimeNano = TimeUnit.NANOSECONDS.convert(runtime, unit);
+            final long maxRuntimeNano = getRuntimeLimitInNanoseconds();
+            return actualRuntimeNano > maxRuntimeNano;
+        }
+    }
+
+    /**
+     * @return the runtime limit in nanoseconds, or -1 if no limit was specified
+     */
+    public long getRuntimeLimitInNanoseconds() {
+        if ( getArguments().maxRuntime == NO_RUNTIME_LIMIT )
+            return -1;
+        else
+            return TimeUnit.NANOSECONDS.convert(getArguments().maxRuntime, getArguments().maxRuntimeUnits);
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 7875ced5a..e2b943582 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.IntervalBinding;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
 import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
@@ -44,6 +45,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.concurrent.TimeUnit;
 
 /**
  * @author aaron
@@ -91,7 +93,7 @@ public class GATKArgumentCollection {
 
     // --------------------------------------------------------------------------------------------------------------
     //
-    // XXX
+    // General features
     //
     // --------------------------------------------------------------------------------------------------------------
 
@@ -143,6 +145,12 @@ public class GATKArgumentCollection {
     @Argument(fullName = "disableRandomization",doc="Completely eliminates randomization from nondeterministic methods. To be used mostly in the testing framework where dynamic parallelism can result in differing numbers of calls to the generator.")
     public boolean disableRandomization = false;
 
+    @Argument(fullName = "maxRuntime", shortName = "maxRuntime", doc="If provided, that GATK will stop execution cleanly as soon after maxRuntime has been exceeded, truncating the run but not exiting with a failure.  By default the value is interpreted in minutes, but this can be changed by maxRuntimeUnits", required = false)
+    public long maxRuntime = GenomeAnalysisEngine.NO_RUNTIME_LIMIT;
+
+    @Argument(fullName = "maxRuntimeUnits", shortName = "maxRuntimeUnits", doc="The TimeUnit for maxRuntime", required = false)
+    public TimeUnit maxRuntimeUnits = TimeUnit.MINUTES;
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // Downsampling Arguments
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
index aa3a1e6ac..547f375bb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
+import java.io.PrintStream;
 
 /**
  * Created with IntelliJ IDEA.
@@ -63,26 +64,24 @@ public class StandardCallerArgumentCollection {
     public int MAX_ALTERNATE_ALLELES = 6;
 
     /**
-     * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
-     * then only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
-     * scales exponentially based on the number of alternate alleles.  Unless there is a good reason to change the default value, we highly recommend
-     * that you not play around with this parameter.
-     *
-     * This argument has been retired in GATK 2.2.  Please specify just maxAltAlleles from now on
+     * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
      */
-    @Deprecated
-    @Hidden
-    @Argument(fullName = "max_alternate_alleles_for_indels", shortName = "maxAltAllelesForIndels", doc = "This argument has been retired in GATK 2.2.  Please specify just maxAltAlleles from now on, which will apply to any variant, regardless of type", required = false)
-    public int MAX_ALTERNATE_ALLELES_FOR_INDELS = -1;
+    @Advanced
+    @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
+    public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
 
     /**
      * If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
      * Basically, it will ignore the contamination fraction of reads for each alternate allele.  So if the pileup contains N total bases, then we
      * will try to remove (N * contamination fraction) bases for each alternate allele.
      */
+    @Argument(fullName = "contamination_fraction_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
+    public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION;
+    public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05;
+
     @Hidden
-    @Argument(fullName = "contamination_percentage_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
-    public double CONTAMINATION_PERCENTAGE = 0.0;
+    @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)
+    public PrintStream contaminationLog = null;
 
     @Hidden
     @Argument(shortName = "logExactCalls", doc="x", required=false)
@@ -96,19 +95,12 @@ public class StandardCallerArgumentCollection {
         this.GenotypingMode = SCAC.GenotypingMode;
         this.heterozygosity = SCAC.heterozygosity;
         this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
-        this.MAX_ALTERNATE_ALLELES_FOR_INDELS = SCAC.MAX_ALTERNATE_ALLELES_FOR_INDELS;
         this.OutputMode = SCAC.OutputMode;
         this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
         this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
-        this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE;
+        this.CONTAMINATION_FRACTION = SCAC.CONTAMINATION_FRACTION;
+        this.contaminationLog = SCAC.contaminationLog;
         this.exactCallsLog = SCAC.exactCallsLog;
         this.AFmodel = SCAC.AFmodel;
     }
-
-    /**
-     * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
-     */
-    @Advanced
-    @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
-    public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 31f2a469c..cc0161b2d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -123,7 +123,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         final ReduceTree reduceTree = new ReduceTree(this);
         initializeWalker(walker);
 
-        while (isShardTraversePending() || isTreeReducePending()) {
+        while (! abortExecution() && (isShardTraversePending() || isTreeReducePending())) {
             // Check for errors during execution.
             errorTracker.throwErrorIfPending();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 5b94e0767..f3c1ae91c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -63,7 +63,7 @@ public class LinearMicroScheduler extends MicroScheduler {
 
         final TraversalEngine traversalEngine = borrowTraversalEngine(this);
         for (Shard shard : shardStrategy ) {
-            if ( done || shard == null ) // we ran out of shards that aren't owned
+            if ( abortExecution() || done || shard == null ) // we ran out of shards that aren't owned
                 break;
 
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index df4ed9ef8..38170040a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
 import org.broadinstitute.sting.gatk.traversals.*;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.AutoFormattingTime;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -52,6 +53,7 @@ import javax.management.ObjectName;
 import java.io.File;
 import java.lang.management.ManagementFactory;
 import java.util.*;
+import java.util.concurrent.TimeUnit;
 
 
 /**
@@ -269,6 +271,26 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
         this.threadEfficiencyMonitor = threadEfficiencyMonitor;
     }
 
+    /**
+     * Should we stop all execution work and exit gracefully?
+     *
+     * Returns true in the case where some external signal or time limit has been received, indicating
+     * that this GATK shouldn't continue executing.  This isn't a kill signal, it is really a "shutdown
+     * gracefully at the next opportunity" signal.  Concrete implementations of the MicroScheduler
+     * examine this value as often as reasonable and, if it returns true, stop what they are doing
+     * at the next available opportunity, shutdown their resources, call notify done, and return.
+     *
+     * @return true if we should abort execution, or false otherwise
+     */
+    protected boolean abortExecution() {
+        final boolean abort = engine.exceedsRuntimeLimit(progressMeter.getRuntimeInNanoseconds(), TimeUnit.NANOSECONDS);
+        if ( abort ) {
+            final AutoFormattingTime aft = new AutoFormattingTime(TimeUnit.SECONDS.convert(engine.getRuntimeLimitInNanoseconds(), TimeUnit.NANOSECONDS), 1, 4);
+            logger.info("Aborting execution (cleanly) because the runtime has exceeded the requested maximum " + aft);
+        }
+        return abort;
+    }
+
     /**
      * Walks a walker over the given list of intervals.
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 2b46414a8..5c7da82d0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -364,7 +364,7 @@ public class VariantContextAdaptors {
 
             long end = hapmap.getEnd();
             if ( deletionLength > 0 )
-                end += deletionLength;
+                end += (deletionLength - 1);
             VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make();
             return vc;
        }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index a68f0df21..18bdb02ed 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 1e1f65333..4d79c4112 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index 3cbca4f52..aef3e49cf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 577b1cfdc..e59fc827d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -1,14 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 4ae1a0bba..0c78c0204 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -34,13 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
index c74f98ca3..1dff4d1a3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index 1cc88fc24..c9481f244 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index d7790969e..89a239e54 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index ec0393cdc..bdf7baec9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 3fe5c5837..07391c78c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index 6487eac50..ca7180510 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -32,8 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index 06fa04526..0340f457c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 5891cbc69..037b357ae 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index 9a4de3c36..dd058b469 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -8,12 +8,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
index 5f405cb46..c67d829c2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.IndelUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index 4be601bc8..c9a4d0ee6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index 85f61c91c..c9d5ca261 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 787c9b29b..82596a501 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,14 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index 74f9c0d0c..364bbdbb9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -7,14 +7,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
index 44657a7e7..afb4ceb60 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
index 21ee66ea2..5f9f3416d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index 8e4edaf0e..3e6aa62a2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index a48d4a678..d75947879 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -7,11 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 680478da0..474b6b150 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -7,16 +7,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 7c7391812..0df7aff71 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -7,15 +7,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MannWhitneyU;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index de0ce2ce2..d01233bb2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -5,7 +5,7 @@ import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index abe55de5a..33e895187 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
index f0bd7ecd9..b3b0be153 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index f6bb4e747..8e1140af1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
index 3d62f2d96..c72ba1c5f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
index 43ef188a8..57b50c6e2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
index c3e98c20f..be7288a7e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index eae13e1b5..ee4f77752 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
index 9c5710872..03fcba760 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
@@ -1,9 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index 6c55c1c00..6970908b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index 738be9883..5b2dc310d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index 2c7a12a36..9506510a9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -25,35 +25,41 @@
 
 package org.broadinstitute.sting.gatk.walkers.bqsr;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.CigarElement;
 import net.sf.samtools.SAMFileHeader;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.Advanced;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
+import org.broadinstitute.sting.gatk.filters.*;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
+import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.recalibration.QuantizationInfo;
-import org.broadinstitute.sting.utils.recalibration.RecalUtils;
-import org.broadinstitute.sting.utils.recalibration.RecalibrationReport;
-import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
+import org.broadinstitute.sting.utils.recalibration.*;
 import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.lang.reflect.Constructor;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context).
@@ -103,19 +109,20 @@ import java.util.ArrayList;
  * </pre>
  */
 
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature(groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class})
 @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
-@By(DataSource.READS)
-@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file
-@Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality
-@PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
-public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long>, NanoSchedulable {
-
+@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
+@PartitionBy(PartitionType.READ)
+public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSchedulable {
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates
 
+    @Advanced
+    @Argument(fullName = "bqsrBAQGapOpenPenalty", shortName="bqsrBAQGOP", doc="BQSR BAQ gap open penalty (Phred Scaled).  Default value is 40.  30 is perhaps better for whole genome call sets", required = false)
+    public double BAQGOP = BAQ.DEFAULT_GOP;
+
     private QuantizationInfo quantizationInfo; // an object that keeps track of the information necessary for quality score quantization
-    
+
     private RecalibrationTables recalibrationTables;
 
     private Covariate[] requestedCovariates; // list to hold the all the covariate objects that were requested (required + standard + experimental)
@@ -124,12 +131,12 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
 
     private int minimumQToUse;
 
-    protected static final String SKIP_RECORD_ATTRIBUTE = "SKIP"; // used to label reads that should be skipped.
-    protected static final String SEEN_ATTRIBUTE = "SEEN"; // used to label reads as processed.
     protected static final String COVARS_ATTRIBUTE = "COVARS"; // used to store covariates array as a temporary attribute inside GATKSAMRecord.\
 
     private static final String NO_DBSNP_EXCEPTION = "This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.";
 
+    private BAQ baq; // BAQ the reads on the fly to generate the alignment uncertainty vector
+    private IndexedFastaSequenceFile referenceReader; // fasta reference reader for use with BAQ calculation
 
     /**
      * Parse the -cov arguments and create a list of covariates to be used here
@@ -137,6 +144,8 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
      */
     public void initialize() {
 
+        baq = new BAQ(BAQGOP); // setup the BAQ object with the provided gap open penalty
+
         // check for unsupported access
         if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals)
             throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
@@ -185,13 +194,21 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         recalibrationEngine.initialize(requestedCovariates, recalibrationTables);
 
         minimumQToUse = getToolkit().getArguments().PRESERVE_QSCORES_LESS_THAN;
+
+        try {
+            // fasta reference reader for use with BAQ calculation
+            referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+        } catch( FileNotFoundException e ) {
+            throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e);
+        }
+
     }
 
     private RecalibrationEngine initializeRecalibrationEngine() {
 
         final Class recalibrationEngineClass = GATKLiteUtils.getProtectedClassIfAvailable(RecalibrationEngine.class);
         try {
-            Constructor constructor = recalibrationEngineClass.getDeclaredConstructor((Class[])null);
+            final Constructor constructor = recalibrationEngineClass.getDeclaredConstructor((Class[])null);
             constructor.setAccessible(true);
             return (RecalibrationEngine)constructor.newInstance();
         }
@@ -200,60 +217,207 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         }
     }
 
-    private boolean readHasBeenSkipped( final GATKSAMRecord read ) {
-        return read.containsTemporaryAttribute(SKIP_RECORD_ATTRIBUTE);
-    }
-
-    private boolean isLowQualityBase( final PileupElement p ) {
-        return p.getQual() < minimumQToUse;
-    }
-
-    private boolean readNotSeen( final GATKSAMRecord read ) {
-        return !read.containsTemporaryAttribute(SEEN_ATTRIBUTE);
+    private boolean isLowQualityBase( final GATKSAMRecord read, final int offset ) {
+        return read.getBaseQualities()[offset] < minimumQToUse;
     }
 
     /**
      * For each read at this locus get the various covariate values and increment that location in the map based on
      * whether or not the base matches the reference at this particular location
-     *
-     * @param tracker the reference metadata tracker
-     * @param ref     the reference context
-     * @param context the alignment context
-     * @return returns 1, but this value isn't used in the reduce step
      */
-    public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        long countedSites = 0L;
-        // Only analyze sites not present in the provided known sites
-        if (tracker.getValues(RAC.knownSites).size() == 0) {
-            for (final PileupElement p : context.getBasePileup()) {
-                final GATKSAMRecord read = p.getRead();
-                final int offset = p.getOffset();
+    public Long map( final ReferenceContext ref, final GATKSAMRecord originalRead, final RefMetaDataTracker metaDataTracker ) {
 
-                // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
-                if (readHasBeenSkipped(read) || p.isInsertionAtBeginningOfRead() || isLowQualityBase(p) )
-                    continue;
+        final GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(originalRead);
+        if( read.isEmpty() ) { return 0L; } // the whole read was inside the adaptor so skip it
 
-                if (readNotSeen(read)) {
-                    read.setTemporaryAttribute(SEEN_ATTRIBUTE, true);
-                    RecalUtils.parsePlatformForRead(read, RAC);
-                    if (!RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) {
-                        read.setTemporaryAttribute(SKIP_RECORD_ATTRIBUTE, true);
-                        continue;
+        RecalUtils.parsePlatformForRead(read, RAC);
+        if (!RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { // parse the solid color space and check for color no-calls
+            return 0L; // skip this read completely
+        }
+        read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates));
+
+        final boolean[] skip = calculateSkipArray(read, metaDataTracker); // skip known sites of variation as well as low quality and non-regular bases
+        final int[] isSNP = calculateIsSNP(read, ref, originalRead);
+        final int[] isInsertion = calculateIsIndel(read, EventType.BASE_INSERTION);
+        final int[] isDeletion = calculateIsIndel(read, EventType.BASE_DELETION);
+        final byte[] baqArray = calculateBAQArray(read);
+
+        if( baqArray != null ) { // some reads just can't be BAQ'ed
+            final double[] snpErrors = calculateFractionalErrorArray(isSNP, baqArray);
+            final double[] insertionErrors = calculateFractionalErrorArray(isInsertion, baqArray);
+            final double[] deletionErrors = calculateFractionalErrorArray(isDeletion, baqArray);
+            recalibrationEngine.updateDataForRead(read, skip, snpErrors, insertionErrors, deletionErrors);
+            return 1L;
+        } else {
+            return 0L;
+        }
+    }
+
+    protected boolean[] calculateSkipArray( final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker ) {
+        final byte[] bases = read.getReadBases();
+        final boolean[] skip = new boolean[bases.length];
+        final boolean[] knownSites = calculateKnownSites(read, metaDataTracker.getValues(RAC.knownSites));
+        for( int iii = 0; iii < bases.length; iii++ ) {
+            skip[iii] = !BaseUtils.isRegularBase(bases[iii]) || isLowQualityBase(read, iii) || knownSites[iii] || badSolidOffset(read, iii);
+        }
+        return skip;
+    }
+
+    protected boolean badSolidOffset( final GATKSAMRecord read, final int offset ) {
+        return ReadUtils.isSOLiDRead(read) && RAC.SOLID_RECAL_MODE != RecalUtils.SOLID_RECAL_MODE.DO_NOTHING && !RecalUtils.isColorSpaceConsistent(read, offset);
+    }
+
+    protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
+        final int BUFFER_SIZE = 0;
+        final int readLength = read.getReadBases().length;
+        final boolean[] knownSites = new boolean[readLength];
+        Arrays.fill(knownSites, false);
+        for( final Feature f : features ) {
+            int featureStartOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getStart(), ReadUtils.ClippingTail.LEFT_TAIL, true); // BUGBUG: should I use LEFT_TAIL here?
+            if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { featureStartOnRead = 0; }
+            int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getEnd(), ReadUtils.ClippingTail.LEFT_TAIL, true);
+            if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { featureEndOnRead = readLength; }
+            Arrays.fill(knownSites, Math.max(0, featureStartOnRead - BUFFER_SIZE), Math.min(readLength, featureEndOnRead + 1 + BUFFER_SIZE), true);
+        }
+        return knownSites;
+    }
+
+    // BUGBUG: can be merged with calculateIsIndel
+    protected static int[] calculateIsSNP( final GATKSAMRecord read, final ReferenceContext ref, final GATKSAMRecord originalRead ) {
+        final byte[] readBases = read.getReadBases();
+        final byte[] refBases = Arrays.copyOfRange(ref.getBases(), read.getAlignmentStart() - originalRead.getAlignmentStart(), ref.getBases().length + read.getAlignmentEnd() - originalRead.getAlignmentEnd());
+        final int[] snp = new int[readBases.length];
+        int readPos = 0;
+        int refPos = 0;
+        for ( final CigarElement ce : read.getCigar().getCigarElements() ) {
+            final int elementLength = ce.getLength();
+            switch (ce.getOperator()) {
+                case M:
+                case EQ:
+                case X:
+                    for( int iii = 0; iii < elementLength; iii++ ) {
+                        snp[readPos] = ( BaseUtils.basesAreEqual(readBases[readPos], refBases[refPos]) ? 0 : 1 );
+                        readPos++;
+                        refPos++;
                     }
-                    read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates));
-                }
-
-                // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
-                if (!ReadUtils.isSOLiDRead(read) ||
-                    RAC.SOLID_RECAL_MODE == RecalUtils.SOLID_RECAL_MODE.DO_NOTHING ||
-                        RecalUtils.isColorSpaceConsistent(read, offset))
-                    // This base finally passed all the checks for a good base, so add it to the big data hashmap
-                    recalibrationEngine.updateDataForPileupElement(p, ref.getBase());
+                    break;
+                case D:
+                case N:
+                    refPos += elementLength;
+                    break;
+                case I:
+                case S: // ReferenceContext doesn't have the soft clipped bases!
+                    readPos += elementLength;
+                    break;
+                case H:
+                case P:
+                    break;
+                default:
+                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
             }
-            countedSites++;
+        }
+        return snp;
+    }
+
+    protected static int[] calculateIsIndel( final GATKSAMRecord read, final EventType mode ) {
+        final byte[] readBases = read.getReadBases();
+        final int[] indel = new int[readBases.length];
+        Arrays.fill(indel, 0);
+        int readPos = 0;
+        for ( final CigarElement ce : read.getCigar().getCigarElements() ) {
+            final int elementLength = ce.getLength();
+            switch (ce.getOperator()) {
+                case M:
+                case EQ:
+                case X:
+                case S:
+                {
+                    readPos += elementLength;
+                    break;
+                }
+                case D:
+                {
+                    final int index = ( read.getReadNegativeStrandFlag() ? readPos : ( readPos > 0 ? readPos - 1 : readPos ) );
+                    indel[index] = ( mode.equals(EventType.BASE_DELETION) ? 1 : 0 );
+                    break;
+                }
+                case I:
+                {
+                    final boolean forwardStrandRead = !read.getReadNegativeStrandFlag();
+                    if( forwardStrandRead ) {
+                        indel[(readPos > 0 ? readPos - 1 : readPos)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
+                    }
+                    for (int iii = 0; iii < elementLength; iii++) {
+                        readPos++;
+                    }
+                    if( !forwardStrandRead ) {
+                        indel[(readPos < indel.length ? readPos : readPos - 1)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
+                    }
+                    break;
+                }
+                case N:
+                case H:
+                case P:
+                    break;
+                default:
+                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
+            }
+        }
+        return indel;
+    }
+
+    protected static double[] calculateFractionalErrorArray( final int[] errorArray, final byte[] baqArray ) {
+        if(errorArray.length != baqArray.length ) {
+            throw new ReviewedStingException("Array length mismatch detected. Malformed read?");
         }
 
-        return countedSites;
+        final byte NO_BAQ_UNCERTAINTY = (byte)'@';
+        final int BLOCK_START_UNSET = -1;
+
+        final double[] fractionalErrors = new double[baqArray.length];
+        Arrays.fill(fractionalErrors, 0.0);
+        boolean inBlock = false;
+        int blockStartIndex = BLOCK_START_UNSET;
+        int iii;
+        for( iii = 0; iii < fractionalErrors.length; iii++ ) {
+            if( baqArray[iii] == NO_BAQ_UNCERTAINTY ) {
+                if( !inBlock ) {
+                    fractionalErrors[iii] = (double) errorArray[iii];
+                } else {
+                    calculateAndStoreErrorsInBlock(iii, blockStartIndex, errorArray, fractionalErrors);
+                    inBlock = false; // reset state variables
+                    blockStartIndex = BLOCK_START_UNSET; // reset state variables
+                }
+            } else {
+                inBlock = true;
+                if( blockStartIndex == BLOCK_START_UNSET ) { blockStartIndex = iii; }
+            }
+        }
+        if( inBlock ) {
+            calculateAndStoreErrorsInBlock(iii-1, blockStartIndex, errorArray, fractionalErrors);
+        }
+        if( fractionalErrors.length != errorArray.length ) {
+            throw new ReviewedStingException("Output array length mismatch detected. Malformed read?");
+        }
+        return fractionalErrors;
+    }
+
+    private static void calculateAndStoreErrorsInBlock( final int iii,
+                                                        final int blockStartIndex,
+                                                        final int[] errorArray,
+                                                        final double[] fractionalErrors ) {
+        int totalErrors = 0;
+        for( int jjj = Math.max(0,blockStartIndex-1); jjj <= iii; jjj++ ) {
+            totalErrors += errorArray[jjj];
+        }
+        for( int jjj = Math.max(0, blockStartIndex-1); jjj <= iii; jjj++ ) {
+            fractionalErrors[jjj] = ((double) totalErrors) / ((double)(iii - Math.max(0,blockStartIndex-1) + 1));
+        }
+    }
+
+    private byte[] calculateBAQArray( final GATKSAMRecord read ) {
+        baq.baqRead(read, referenceReader, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.ADD_TAG);
+        return BAQ.getBAQTag(read);
     }
 
     /**
@@ -277,11 +441,6 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         return sum;
     }
 
-    public Long treeReduce(Long sum1, Long sum2) {
-        sum1 += sum2;
-        return sum1;
-    }
-
     @Override
     public void onTraversalDone(Long result) {
         logger.info("Calculating quantized quality scores...");
@@ -291,12 +450,12 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         generateReport();
         logger.info("...done!");
 
-        if (RAC.RECAL_PDF_FILE != null) {
+        if ( RAC.RECAL_PDF_FILE != null ) {
             logger.info("Generating recalibration plots...");
             generatePlots();
         }
 
-        logger.info("Processed: " + result + " sites");
+        logger.info("Processed: " + result + " reads");
     }
 
     private void generatePlots() {
@@ -309,7 +468,6 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
             RecalUtils.generateRecalibrationPlot(RAC, recalibrationTables, requestedCovariates);
     }
 
-
     /**
      * go through the quality score table and use the # observations and the empirical quality score
      * to build a quality score histogram for quantization. Then use the QuantizeQual algorithm to
@@ -322,5 +480,4 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
     private void generateReport() {
         RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates);
     }
-}
-
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
index ce60f5a3a..962d62d5e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
@@ -33,7 +33,5 @@ public interface RecalibrationEngine {
 
     public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables);
 
-    public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase);
-
     public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors);
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
index 4fe9c5323..6031aa955 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
@@ -46,57 +46,32 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
         this.recalibrationTables = recalibrationTables;
     }
 
-    /**
-     * Loop through the list of requested covariates and pick out the value from the read, offset, and reference
-     * Using the list of covariate values as a key, pick out the RecalDatum and increment,
-     * adding one to the number of observations and potentially one to the number of mismatches for mismatches only.
-     *
-     * @param pileupElement The pileup element to update
-     * @param refBase       The reference base at this locus
-     */
     @Override
-    public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {
-        final int offset = pileupElement.getOffset();
-        final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead());
+    public void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
+        for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
+            if( !skip[offset] ) {
+                final ReadCovariates readCovariates = covariateKeySetFrom(read);
 
-        final byte qual = pileupElement.getQual();
-        final boolean isError = !BaseUtils.basesAreEqual(pileupElement.getBase(), refBase);
+                final byte qual = read.getBaseQualities()[offset];
+                final double isError = snpErrors[offset];
 
-        final int[] keys = readCovariates.getKeySet(offset, EventType.BASE_SUBSTITUTION);
-        final int eventIndex = EventType.BASE_SUBSTITUTION.index;
+                final int[] keys = readCovariates.getKeySet(offset, EventType.BASE_SUBSTITUTION);
+                final int eventIndex = EventType.BASE_SUBSTITUTION.index;
 
-        final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getReadGroupTable();
-        final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
-        final RecalDatum rgThisDatum = createDatumObject(qual, isError);
-        if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
-            rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
-        else
-            rgPreviousDatum.combine(rgThisDatum);
+                combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex);
 
-        final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getQualityScoreTable();
-        final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
-        if (qualPreviousDatum == null)
-            qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
-        else
-            qualPreviousDatum.increment(isError);
+                incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex);
 
-        for (int i = 2; i < covariates.length; i++) {
-            if (keys[i] < 0)
-                continue;
-            final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
-            final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
-            if (covPreviousDatum == null)
-                covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
-            else
-                covPreviousDatum.increment(isError);
+                for (int i = 2; i < covariates.length; i++) {
+                    if (keys[i] < 0)
+                        continue;
+
+                    incrementDatumOrPutIfNecessary(recalibrationTables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
+                }
+            }
         }
     }
 
-    @Override
-    public synchronized void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
-        throw new UnsupportedOperationException("Delocalized BQSR is not available in the GATK-lite version");
-    }
-
     /**
      * creates a datum object with one observation and one or zero error
      *
@@ -104,10 +79,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
      * @param isError       whether or not the observation is an error
      * @return a new RecalDatum object with the observation and the error
      */
-    protected RecalDatum createDatumObject(final byte reportedQual, final boolean isError) {
-        return new RecalDatum(1, isError ? 1:0, reportedQual);
-    }
-
     protected RecalDatum createDatumObject(final byte reportedQual, final double isError) {
         return new RecalDatum(1, isError, reportedQual);
     }
@@ -121,4 +92,63 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
     protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
         return (ReadCovariates) read.getTemporaryAttribute(BaseRecalibrator.COVARS_ATTRIBUTE);
     }
+
+    /**
+     * Increments the RecalDatum at the specified position in the specified table, or put a new item there
+     * if there isn't already one.
+     *
+     * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put()
+     * to return false if another thread inserts a new item at our position in the middle of our put operation.
+     *
+     * @param table the table that holds/will hold our item
+     * @param qual qual for this event
+     * @param isError error value for this event
+     * @param keys location in table of our item
+     */
+    protected void incrementDatumOrPutIfNecessary( final NestedIntegerArray<RecalDatum> table, final byte qual, final double isError, final int... keys ) {
+        final RecalDatum existingDatum = table.get(keys);
+
+        if ( existingDatum == null ) {
+            // No existing item, try to put a new one
+            if ( ! table.put(createDatumObject(qual, isError), keys) ) {
+                // Failed to put a new item because another thread came along and put an item here first.
+                // Get the newly-put item and increment it (item is guaranteed to exist at this point)
+                table.get(keys).increment(1.0, isError);
+            }
+        }
+        else {
+            // Easy case: already an item here, so increment it
+            existingDatum.increment(1.0, isError);
+        }
+    }
+
+    /**
+     * Combines the RecalDatum at the specified position in the specified table with a new RecalDatum, or put a
+     * new item there if there isn't already one.
+     *
+     * Does this in a thread-safe way WITHOUT being synchronized: relies on the behavior of NestedIntegerArray.put()
+     * to return false if another thread inserts a new item at our position in the middle of our put operation.
+     *
+     * @param table the table that holds/will hold our item
+     * @param qual qual for this event
+     * @param isError error value for this event
+     * @param keys location in table of our item
+     */
+    protected void combineDatumOrPutIfNecessary( final NestedIntegerArray<RecalDatum> table, final byte qual, final double isError, final int... keys ) {
+        final RecalDatum existingDatum = table.get(keys);
+        final RecalDatum newDatum = createDatumObject(qual, isError);
+
+        if ( existingDatum == null ) {
+            // No existing item, try to put a new one
+            if ( ! table.put(newDatum, keys) ) {
+                // Failed to put a new item because another thread came along and put an item here first.
+                // Get the newly-put item and combine it with our item (item is guaranteed to exist at this point)
+                table.get(keys).combine(newDatum);
+            }
+        }
+        else {
+            // Easy case: already an item here, so combine it with our item
+            existingDatum.combine(newDatum);
+        }
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 77da35c41..ae9b01f2d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -104,7 +104,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
                                                    final List<Allele> allAllelesToUse,
                                                    final boolean useBAQedPileup,
                                                    final GenomeLocParser locParser,
-                                                   final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap);
+                                                   final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap);
 
 
     protected int getFilteredDepth(ReadBackedPileup pileup) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1761f9cec..0d9f443e2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Haplotype;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -81,7 +82,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                          final List<Allele> allAllelesToUse,
                                          final boolean useBAQedPileup,
                                          final GenomeLocParser locParser,
-                                         final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                         final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
 
         GenomeLoc loc = ref.getLocus();
 //        if (!ref.getLocus().equals(lastSiteVisited)) {
@@ -118,12 +119,12 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
             }
             final ReadBackedPileup pileup = context.getBasePileup();
             if (pileup != null) {
                 final GenotypeBuilder b = new GenotypeBuilder(sample.getKey());
-                final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()));
+                final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()), UAC.CONTAMINATION_FRACTION, UAC.contaminationLog);
                 b.PL(genotypeLikelihoods);
                 b.DP(getFilteredDepth(pileup));
                 genotypes.add(b.make());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index d053e13a8..791cdc325 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 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.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
@@ -48,13 +49,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
     private final boolean useAlleleFromVCF;
 
     private final double[] likelihoodSums = new double[4];
-    private final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
+
+    private final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;
 
     protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
         useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-        for ( int i = 0; i < 4; i++ )
-            alleleStratifiedElements[i] = new ArrayList<PileupElement>();
+        perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
     }
 
     public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
@@ -64,9 +65,9 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
                                          final List<Allele> allAllelesToUse,
                                          final boolean useBAQedPileup,
                                          final GenomeLocParser locParser,
-                                         final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                         final Map<String, PerReadAlleleLikelihoodMap> sampleLikelihoodMap) {
 
-        perReadAlleleLikelihoodMap.clear(); // not used in SNP model, sanity check to delete any older data
+        sampleLikelihoodMap.clear(); // not used in SNP model, sanity check to delete any older data
 
         final byte refBase = ref.getBase();
         final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase);
@@ -79,8 +80,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size());
         for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {
             ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
-            if ( UAC.CONTAMINATION_PERCENTAGE > 0.0 )
-                pileup = createDecontaminatedPileup(pileup, UAC.CONTAMINATION_PERCENTAGE);
+            if ( UAC.CONTAMINATION_FRACTION > 0.0 )
+                pileup = perReadAlleleLikelihoodMap.createPerAlleleDownsampledBasePileup(pileup, UAC.CONTAMINATION_FRACTION, UAC.contaminationLog);
             if ( useBAQedPileup )
                 pileup = createBAQedPileup(pileup);
 
@@ -203,42 +204,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         return allelesToUse;
     }
 
-    public ReadBackedPileup createDecontaminatedPileup(final ReadBackedPileup pileup, final double contaminationPercentage) {
-        // special case removal of all reads
-        if ( contaminationPercentage >= 1.0 )
-            return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
-
-        // start by stratifying the reads by the alleles they represent at this position
-        for( final PileupElement pe : pileup ) {
-            final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
-            if ( baseIndex != -1 )
-                alleleStratifiedElements[baseIndex].add(pe);
-        }
-
-        // Down-sample *each* allele by the contamination fraction applied to the entire pileup.
-        // Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later.
-        int numReadsToRemove = (int)Math.ceil((double)pileup.getNumberOfElements() * contaminationPercentage);
-        final TreeSet<PileupElement> elementsToKeep = new TreeSet<PileupElement>(new Comparator<PileupElement>() {
-            @Override
-            public int compare(PileupElement element1, PileupElement element2) {
-                final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
-                return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
-            }
-        });
-
-        for ( int i = 0; i < 4; i++ ) {
-            final ArrayList<PileupElement> alleleList = alleleStratifiedElements[i];
-            if ( alleleList.size() > numReadsToRemove )
-                elementsToKeep.addAll(downsampleElements(alleleList, numReadsToRemove));
-        }
-
-        // clean up pointers so memory can be garbage collected if needed
-        for ( int i = 0; i < 4; i++ )
-            alleleStratifiedElements[i].clear();
-
-        return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>(elementsToKeep));
-    }
-
     public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pileup ) {
         final List<PileupElement> BAQedElements = new ArrayList<PileupElement>();
         for( final PileupElement PE : pileup ) {
@@ -257,22 +222,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         public byte getQual( final int offset ) { return BAQ.calcBAQFromTag(getRead(), offset, true); }
     }
 
-    private List<PileupElement> downsampleElements(final ArrayList<PileupElement> elements, final int numElementsToRemove) {
-        final int pileupSize = elements.size();
-        final BitSet itemsToRemove = new BitSet(pileupSize);
-        for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
-            itemsToRemove.set(selectedIndex);
-        }
-
-        ArrayList<PileupElement> elementsToKeep = new ArrayList<PileupElement>(pileupSize - numElementsToRemove);
-        for ( int i = 0; i < pileupSize; i++ ) {
-            if ( !itemsToRemove.get(i) )
-                elementsToKeep.add(elements.get(i));
-        }
-
-        return elementsToKeep;
-    }
-
     private static class SampleGenotypeData {
 
         public final String name;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index e50f25fe8..5f6ddf0f1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -47,8 +47,8 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
     /**
      * Note that calculating the SLOD increases the runtime by an appreciable amount.
      */
-    @Argument(fullName = "noSLOD", shortName = "nosl", doc = "If provided, we will not calculate the SLOD", required = false)
-    public boolean NO_SLOD = false;
+    @Argument(fullName = "computeSLOD", shortName = "slod", doc = "If provided, we will calculate the SLOD (SB annotation)", required = false)
+    public boolean COMPUTE_SLOD = false;
 
     /**
      * Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
@@ -204,7 +204,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
         this.GLmodel = uac.GLmodel;
         this.AFmodel = uac.AFmodel;
         this.PCR_error = uac.PCR_error;
-        this.NO_SLOD = uac.NO_SLOD;
+        this.COMPUTE_SLOD = uac.COMPUTE_SLOD;
         this.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
         this.MIN_BASE_QUALTY_SCORE = uac.MIN_BASE_QUALTY_SCORE;
         this.MAX_DELETION_FRACTION = uac.MAX_DELETION_FRACTION;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 3116d3a7d..36be2e7c6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
@@ -234,36 +235,26 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY ||
                     UAC.referenceSampleName != null ||
                     UAC.referenceSampleRod.isBound())  {
-                throw new UserException.NotSupportedInGATKLite("Usage of ploidy values different than 2 not supported in this GATK version");
+                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
             }
+
+            if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
+                if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) {
+                    UAC.CONTAMINATION_FRACTION = 0.0;
+                    logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite");
+                } else {
+                    throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
+                }
+            }
+        }
+
+        if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) {
+            samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
+        } else {
             // get all of the unique sample names
             samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-
-        } else {
-            // in full mode: check for consistency in ploidy/pool calling arguments
-            // check for correct calculation models
-/*            if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
-                // polyploidy requires POOL GL and AF calculation models to be specified right now
-                if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL
-                        && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH)   {
-                    throw new UserException("Incorrect genotype calculation model chosen. Only [POOLSNP|POOLINDEL|POOLBOTH] supported with this walker if sample ploidy != 2");
-                }
-
-                if (UAC.AFmodel != AFCalc.Model.POOL)
-                    throw new UserException("Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2");
-
-            }
-  */
-            // get all of the unique sample names
-            if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
-                samples.clear();
-                samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
-            } else {
-                samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-                if (UAC.referenceSampleName != null )
-                    samples.remove(UAC.referenceSampleName);
-            }
-
+            if ( UAC.referenceSampleName != null )
+                samples.remove(UAC.referenceSampleName);
         }
 
         // check for a bad max alleles value
@@ -305,7 +296,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
 
         // annotation (INFO) fields from UnifiedGenotyper
-        if ( !UAC.NO_SLOD )
+        if ( UAC.COMPUTE_SLOD )
             VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.STRAND_BIAS_KEY);
 
         if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index a52b5dfe6..97254c478 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -153,19 +153,19 @@ public class UnifiedGenotyperEngine {
     }
 
 
-        /**
-        * Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper.
-        *
-        * If allSamples != null, then the output variantCallContext is guarenteed to contain a genotype
-        * for every sample in allSamples.  If it's null there's no such guarentee.  Providing this
-        * argument is critical when the resulting calls will be written to a VCF file.
-        *
-        * @param tracker    the meta data tracker
-        * @param refContext the reference base
-        * @param rawContext contextual information around the locus
-        * @param allSamples set of all sample names that we might call (i.e., those in the VCF header)
-        * @return the VariantCallContext object
-        */
+    /**
+     * Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper.
+     *
+     * If allSamples != null, then the output variantCallContext is guarenteed to contain a genotype
+     * for every sample in allSamples.  If it's null there's no such guarentee.  Providing this
+     * argument is critical when the resulting calls will be written to a VCF file.
+     *
+     * @param tracker    the meta data tracker
+     * @param refContext the reference base
+     * @param rawContext contextual information around the locus
+     * @param allSamples set of all sample names that we might call (i.e., those in the VCF header)
+     * @return the VariantCallContext object
+     */
     public List<VariantCallContext> calculateLikelihoodsAndGenotypes(final RefMetaDataTracker tracker,
                                                                      final ReferenceContext refContext,
                                                                      final AlignmentContext rawContext,
@@ -174,7 +174,7 @@ public class UnifiedGenotyperEngine {
 
         final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
 
-        final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = new HashMap<String,PerReadAlleleLikelihoodMap>();
+        final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = new HashMap<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap>();
 
         if ( models.isEmpty() ) {
             results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null);
@@ -209,7 +209,7 @@ public class UnifiedGenotyperEngine {
     public VariantContext calculateLikelihoods(final RefMetaDataTracker tracker,
                                                final ReferenceContext refContext,
                                                final AlignmentContext rawContext,
-                                               final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                               final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
         final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
         if ( models.isEmpty() ) {
             return null;
@@ -275,7 +275,7 @@ public class UnifiedGenotyperEngine {
                                                 final List<Allele> alternateAllelesToUse,
                                                 final boolean useBAQedPileup,
                                                 final GenotypeLikelihoodsCalculationModel.Model model,
-                                                final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                                final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
 
         // initialize the data for this thread if that hasn't been done yet
         if ( glcm.get() == null ) {
@@ -313,7 +313,7 @@ public class UnifiedGenotyperEngine {
         return new VariantCallContext(vc, false);
     }
 
-    public VariantCallContext calculateGenotypes(final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+    public VariantCallContext calculateGenotypes(final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
         return calculateGenotypes(null, null, null, null, vc, model, perReadAlleleLikelihoodMap);
     }
 
@@ -327,7 +327,7 @@ public class UnifiedGenotyperEngine {
                                                  final Map<String, AlignmentContext> stratifiedContexts,
                                                  final VariantContext vc,
                                                  final GenotypeLikelihoodsCalculationModel.Model model,
-                                                 final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                                 final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
         return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false,perReadAlleleLikelihoodMap);
     }
 
@@ -346,7 +346,7 @@ public class UnifiedGenotyperEngine {
                                                  final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,
                                                  final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model,
                                                  final boolean inheritAttributesFromInputVC,
-                                                 final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
+                                                 final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
 
         boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;
 
@@ -451,7 +451,7 @@ public class UnifiedGenotyperEngine {
             attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies);
         }
 
-        if ( !UAC.NO_SLOD && !limitedContext && !bestGuessIsRef ) {
+        if ( UAC.COMPUTE_SLOD && !limitedContext && !bestGuessIsRef ) {
             //final boolean DEBUG_SLOD = false;
 
             // the overall lod
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 3d287057c..79962a3e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 
 import com.google.java.contract.Ensures;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
@@ -41,8 +41,8 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.io.PrintStream;
 import java.util.Arrays;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
@@ -188,11 +188,14 @@ public class PairHMMIndelErrorModel {
                                                                         final LinkedHashMap<Allele, Haplotype> haplotypeMap,
                                                                         final ReferenceContext ref,
                                                                         final int eventLength,
-                                                                        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
+                                                                        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap,
+                                                                        final double downsamplingFraction,
+                                                                        final PrintStream downsamplingLog) {
         final int numHaplotypes = haplotypeMap.size();
 
         final int readCounts[] = new int[pileup.getNumberOfElements()];
         final double[][] readLikelihoods = computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap, readCounts);
+        perReadAlleleLikelihoodMap.performPerAlleleDownsampling(downsamplingFraction, downsamplingLog);
         return getDiploidHaplotypeLikelihoods(numHaplotypes, readCounts, readLikelihoods);
         
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index 7c73f59e9..0165c6cf3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
@@ -438,8 +438,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 
 		location = getToolkit().getGenomeLocParser().createGenomeLoc(getToolkit().getSAMFileHeader().getSequence(0).getSequenceName(),1);
 
-        normalSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeaders().get(0));
-
         try {
             // we already checked that bedOutput and output_file are not set simultaneously
             if ( bedOutput != null ) bedWriter = new FileWriter(bedOutput);
@@ -1152,8 +1150,9 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 
         GenotypesContext genotypes = GenotypesContext.create();
         for ( String sample : normalSamples ) {
-            final GenotypeBuilder gb = new GenotypeBuilder(sample);
-            gb.attributes(call.makeStatsAttributes(null));
+            GenotypeBuilder gb = new GenotypeBuilder(sample);
+
+            gb=call.addStatsAttributes(gb);
             gb.alleles(! discard_event
                 ? alleles             // we made a call - put actual het genotype here:
                 : homref_alleles);    // no call: genotype is ref/ref (but alleles still contain the alt if we observed anything at all)
@@ -1200,8 +1199,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
         if ( start == 0 )
             return;
 
-        Map<String,Object> attrsNormal = nCall.makeStatsAttributes(null);
-        Map<String,Object> attrsTumor = tCall.makeStatsAttributes(null);
+        GenotypeBuilder nGB = new GenotypeBuilder();
+        GenotypeBuilder tGB = new GenotypeBuilder();
+
+        nCall.addStatsAttributes(nGB);
+        tCall.addStatsAttributes(tGB);
 
         Map<String,Object> attrs = new HashMap();
 
@@ -1242,11 +1244,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
         GenotypesContext genotypes = GenotypesContext.create();
 
         for ( String sample : normalSamples ) {
-            genotypes.add(GenotypeBuilder.create(sample, homRefN ? homRefAlleles : alleles, attrsNormal));
+            genotypes.add(nGB.name(sample).alleles(homRefN ? homRefAlleles : alleles).make());
         }
 
         for ( String sample : tumorSamples ) {
-            genotypes.add(GenotypeBuilder.create(sample, homRefT ? homRefAlleles : alleles, attrsTumor));
+            genotypes.add(tGB.name(sample).alleles(homRefT ? homRefAlleles : alleles).make());
         }
 
         Set<String> filters = null;
@@ -1254,14 +1256,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
             filters = new HashSet<String>();
             filters.add("NoCall");
         }
-        if ( nCall.getCoverage() < minNormalCoverage ) {
-            if ( filters == null ) filters = new HashSet<String>();
-            filters.add("NCov");
-        }
-        if ( tCall.getCoverage() < minCoverage ) {
-            if ( filters == null ) filters = new HashSet<String>();
-            filters.add("TCov");
-        }
 
         VariantContext vc = new VariantContextBuilder("IGv2_Indel_call", refName, start, stop, alleles)
                 .genotypes(genotypes).filters(filters).attributes(attrs).make();
@@ -1844,6 +1838,38 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
              VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,attr);
              return attr;
          }
+
+
+    /**
+      * Adds alignment statistics directly into the genotype builder object.
+      *
+      * @param gb
+      * @return
+      */
+     public GenotypeBuilder addStatsAttributes(GenotypeBuilder gb) {
+          if ( gb == null ) gb = new GenotypeBuilder();
+
+          gb = VCFIndelAttributes.recordDepth(getConsensusVariantCount(),getAllVariantCount(),getCoverage(),gb);
+
+          gb = VCFIndelAttributes.recordAvMM(getAvConsensusMismatches(),getAvRefMismatches(),gb);
+
+          gb = VCFIndelAttributes.recordAvMapQ(getAvConsensusMapq(),getAvRefMapq(),gb);
+
+          gb = VCFIndelAttributes.recordNQSMMRate(getNQSConsensusMMRate(),getNQSRefMMRate(),gb);
+
+          gb = VCFIndelAttributes.recordNQSAvQ(getNQSConsensusAvQual(),getNQSRefAvQual(),gb);
+
+          gb = VCFIndelAttributes.recordOffsetFromStart(from_start_median,from_start_mad,gb);
+
+          gb = VCFIndelAttributes.recordOffsetFromEnd(from_end_median,from_end_mad,gb);
+
+          PrimitivePair.Int strand_cons = getConsensusStrandCounts();
+          PrimitivePair.Int strand_ref = getRefStrandCounts();
+
+          gb = VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,gb);
+          return gb;
+      }
+
     }
 
     interface IndelListener {
@@ -2170,18 +2196,18 @@ class VCFIndelAttributes {
     public static Set<? extends VCFHeaderLine> getAttributeHeaderLines() {
         Set<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
 
-        lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus indel/reference at the site"));
+        lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus reference/indel at the site"));
         lines.add(new VCFFormatHeaderLine(DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, "Total coverage at the site"));
 
-        lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of consensus indel-supporting reads/reference-supporting reads"));
+        lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of ref-/consensus indel-supporting reads"));
 
-        lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per consensus indel-supporting read/per reference-supporting read"));
+        lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per ref-/consensus indel-supporting read"));
 
-        lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in consensus indel-supporting reads/in reference-supporting reads"));
+        lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads"));
 
-        lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases from consensus indel-supporting reads/from reference-supporting reads"));
+        lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases in ref-/consensus indel-supporting reads"));
 
-        lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned indel-supporting reads / forward-/reverse-aligned reference supporting reads"));
+        lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)"));
 
         lines.add(new VCFFormatHeaderLine(RSTART_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the starts of the reads"));
         lines.add(new VCFFormatHeaderLine(REND_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the ends of the reads"));
@@ -2194,39 +2220,72 @@ class VCFIndelAttributes {
         return attrs;
     }
 
+    public static GenotypeBuilder recordStrandCounts(int cnt_cons_fwd, int cnt_cons_rev, int cnt_ref_fwd, int cnt_ref_rev,
+                                                     GenotypeBuilder gb) {
+        return gb.attribute(STRAND_COUNT_KEY, new Integer[] {cnt_ref_fwd, cnt_ref_rev,cnt_cons_fwd, cnt_cons_rev } );
+    }
+
     public static Map<String,Object> recordDepth(int cnt_cons, int cnt_indel, int cnt_total, Map<String,Object> attrs) {
-        attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_cons, cnt_indel} );
+        attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_total-cnt_indel, cnt_cons} );
         attrs.put(DEPTH_TOTAL_KEY, cnt_total);
         return attrs;
     }
 
+    public static GenotypeBuilder recordDepth(int cnt_cons, int cnt_indel, int cnt_total, GenotypeBuilder gb) {
+        return gb.AD(new int[] {cnt_total-cnt_indel,cnt_cons} ).DP(cnt_total);
+    }
+
     public static Map<String,Object> recordAvMapQ(double cons, double ref, Map<String,Object> attrs) {
-        attrs.put(MAPQ_KEY, new Float[] {(float)cons, (float)ref} );
+        attrs.put(MAPQ_KEY, new Float[] {(float)ref, (float)cons} );
         return attrs;
     }
 
+    public static GenotypeBuilder recordAvMapQ(double cons, double ref, GenotypeBuilder gb) {
+        return gb.attribute(MAPQ_KEY,new float[] {(float)ref, (float)cons} );
+    }
+
     public static Map<String,Object> recordAvMM(double cons, double ref, Map<String,Object> attrs) {
-        attrs.put(MM_KEY, new Float[] {(float)cons, (float)ref} );
+        attrs.put(MM_KEY, new Float[] {(float)ref, (float)cons} );
         return attrs;
     }
 
+    public static GenotypeBuilder recordAvMM(double cons, double ref, GenotypeBuilder gb) {
+        return gb.attribute(MM_KEY, new float[] {(float)ref, (float)cons} );
+    }
+
     public static Map<String,Object> recordNQSMMRate(double cons, double ref, Map<String,Object> attrs) {
-        attrs.put(NQS_MMRATE_KEY, new Float[] {(float)cons, (float)ref} );
+        attrs.put(NQS_MMRATE_KEY, new Float[] {(float)ref, (float)cons} );
         return attrs;
     }
 
+    public static GenotypeBuilder recordNQSMMRate(double cons, double ref, GenotypeBuilder gb) {
+        return gb.attribute(NQS_MMRATE_KEY, new float[] {(float)ref, (float)cons} );
+    }
+
     public static Map<String,Object> recordNQSAvQ(double cons, double ref, Map<String,Object> attrs) {
-        attrs.put(NQS_AVQ_KEY, new Float[] {(float)cons, (float)ref} );
+        attrs.put(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
         return attrs;
     }
 
+    public static GenotypeBuilder recordNQSAvQ(double cons, double ref, GenotypeBuilder gb) {
+        return gb.attribute(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
+    }
+
     public static Map<String,Object> recordOffsetFromStart(int median, int mad, Map<String,Object> attrs) {
         attrs.put(RSTART_OFFSET_KEY, new Integer[] {median, mad} );
         return attrs;
     }
 
+    public static GenotypeBuilder recordOffsetFromStart(int median, int mad, GenotypeBuilder gb) {
+        return gb.attribute(RSTART_OFFSET_KEY, new int[] {median, mad} );
+    }
+
     public static Map<String,Object> recordOffsetFromEnd(int median, int mad, Map<String,Object> attrs) {
         attrs.put(REND_OFFSET_KEY, new Integer[] {median, mad} );
         return attrs;
     }
+
+    public static GenotypeBuilder recordOffsetFromEnd(int median, int mad, GenotypeBuilder gb) {
+        return gb.attribute(REND_OFFSET_KEY, new int[] {median, mad} );
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
new file mode 100644
index 000000000..78bcf1228
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
@@ -0,0 +1,173 @@
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+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.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Emits intervals in which the differences between the original and reduced bam quals are bigger epsilon (unless the quals of
+ * the reduced bam are above sufficient threshold)
+ *
+ * <h2>Input</h2>
+ * <p>
+ * The original and reduced BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A list of intervals in which the differences between the original and reduced bam quals are bigger epsilon.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -I:original original.bam \
+ *   -I:reduced reduced.bam \
+ *   -R ref.fasta \
+ *   -T AssessReducedQuals \
+ *   -o output.intervals
+ * </pre>
+ *
+ * @author ami
+ */
+
+public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implements TreeReducible<GenomeLoc> {
+
+    private static final String reduced = "reduced";
+    private static final String original = "original";
+    private static final int originalQualsIndex = 0;
+    private static final int reducedQualsIndex = 1;
+
+    @Argument(fullName = "sufficientQualSum", shortName = "sufficientQualSum", doc = "When a reduced bam qual sum is above this threshold, it passes even without comparing to the non-reduced bam ", required = false)
+    public int sufficientQualSum = 600;
+
+    @Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false)
+    public int qual_epsilon = 0;
+
+    @Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on")   // TODO -- best to make this optional
+    public int debugLevel = 0;   // TODO -- best to make this an enum or boolean
+
+    @Output
+    protected PrintStream out;
+
+    public void initialize() {
+        if (debugLevel != 0)
+            out.println("  Debug mode" +
+                        "Debug:\tsufficientQualSum: "+sufficientQualSum+ "\n " +
+                        "Debug:\tqual_epsilon: "+qual_epsilon);
+    }
+
+    @Override
+    public boolean includeReadsWithDeletionAtLoci() { return true; }
+
+    @Override
+    public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null )
+            return null;
+
+        boolean reportLocus;
+        final int[] quals = getPileupQuals(context.getBasePileup());
+        if (debugLevel != 0)
+            out.println("Debug:\tLocus Quals\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]);
+        final int epsilon = MathUtils.fastRound(quals[originalQualsIndex]*qual_epsilon);
+        final int calcOriginalQuals = Math.min(quals[originalQualsIndex],sufficientQualSum);
+        final int calcReducedQuals = Math.min(quals[reducedQualsIndex],sufficientQualSum);
+        final int OriginalReducedQualDiff = calcOriginalQuals - calcReducedQuals;
+        reportLocus = OriginalReducedQualDiff > epsilon || OriginalReducedQualDiff < -1*epsilon;
+        if(debugLevel != 0 && reportLocus)
+            out.println("Debug:\tEmited Locus\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]+"\tepsilon\t"+epsilon+"\tdiff\t"+OriginalReducedQualDiff);
+
+        return reportLocus ? ref.getLocus() : null;
+    }
+
+    private final int[] getPileupQuals(final ReadBackedPileup readPileup) {
+
+        final int[] quals = new int[2];
+        String[] printPileup = {"Debug 2:\toriginal pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n",
+                                "Debug 2:\t reduced pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n"};
+
+        for( PileupElement p : readPileup ){
+            final List<String> tags = getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags();
+            if ( isGoodRead(p,tags) ){
+                final int tempQual = (int)(p.getQual()) * p.getRepresentativeCount();
+                final int tagIndex = getTagIndex(tags);
+                quals[tagIndex] += tempQual;
+                if(debugLevel == 2)
+                    printPileup[tagIndex] += "\tDebug 2: ("+p+")\tMQ="+p.getMappingQual()+":QU="+p.getQual()+":RC="+p.getRepresentativeCount()+":OS="+p.getOffset()+"\n";
+            }
+        }
+        if(debugLevel == 2){
+            out.println(printPileup[originalQualsIndex]);
+            out.println(printPileup[reducedQualsIndex]);
+        }
+        return quals;
+    }
+
+    // TODO -- arguments/variables should be final, not method declaration
+    private final boolean isGoodRead(PileupElement p, List<String> tags){
+        // TODO -- this isn't quite right.  You don't need the tags here.  Instead, you want to check whether the read itself (which
+        // TODO --  you can get from the PileupElement) is a reduced read (not all reads from the reduced bam are reduced) and only
+        // TODO --  for them do you want to ignore that min mapping quality cutoff (but you *do* still want the min base cutoff).
+        return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20));
+    }
+
+    private final int getTagIndex(List<String> tags){
+        return tags.contains(reduced) ? 1 : 0;
+    }
+
+    @Override
+    public void onTraversalDone(GenomeLoc sum) {
+        if ( sum != null )
+            out.println(sum);
+    }
+
+    @Override
+    public GenomeLoc treeReduce(GenomeLoc lhs, GenomeLoc rhs) {
+        if ( lhs == null )
+            return rhs;
+
+        if ( rhs == null )
+            return lhs;
+
+        // if contiguous, just merge them
+        if ( lhs.contiguousP(rhs) )
+            return getToolkit().getGenomeLocParser().createGenomeLoc(lhs.getContig(), lhs.getStart(), rhs.getStop());
+
+        // otherwise, print the lhs and start over with the rhs
+        out.println(lhs);
+        return rhs;
+    }
+
+    @Override
+    public GenomeLoc reduceInit() {
+        return null;
+    }
+
+    @Override
+    public GenomeLoc reduce(GenomeLoc value, GenomeLoc sum) {
+        if ( value == null )
+            return sum;
+
+        if ( sum == null )
+            return value;
+
+        // if contiguous, just merge them
+        if ( sum.contiguousP(value) )
+            return getToolkit().getGenomeLocParser().createGenomeLoc(sum.getContig(), sum.getStart(), value.getStop());
+
+        // otherwise, print the sum and start over with the value
+        out.println(sum);
+        return value;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
index 5beeeb3e6..79b6e17f6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
@@ -245,24 +245,21 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
     @Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
     private int minDepth = -1;
 
-    /**
-     * If your VCF or BAM file has more than one sample and you only want to validate one, use this parameter to choose it.
-     */
-    @Hidden
-    @Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
-    private String sample = "";
-
-    /**
+   /**
      * Print out discordance sites to standard out.
      */
     @Hidden
     @Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false)
-    private boolean printInterestingSites;
+    private boolean printInterestingSites = false;
 
     private UnifiedGenotyperEngine snpEngine;
     private UnifiedGenotyperEngine indelEngine;
     private Set<String> samples;
 
+    private enum GVstatus {
+        T, F, NONE
+    }
+
     public static class CountedData {
         private long nAltCalledAlt = 0L;
         private long nAltCalledRef = 0L;
@@ -336,8 +333,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
         snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
 
         // Adding the INDEL calling arguments for UG
-        uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
-        indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
+        UnifiedArgumentCollection uac_indel = new UnifiedArgumentCollection(uac);
+        uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
+        indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac_indel);
 
         // make sure we have callConf set to the threshold set by the UAC so we can use it later.
         callConf = uac.STANDARD_CONFIDENCE_FOR_CALLING;
@@ -368,9 +366,10 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
         // Do not operate on variants that are not covered to the optional minimum depth
         if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
             counter.nUncovered = 1L;
-            if (vcComp.getAttribute("GV").equals("T"))
+            final GVstatus status = getGVstatus(vcComp);
+            if ( status == GVstatus.T )
                 counter.nAltNotCalled = 1L;
-            else if (vcComp.getAttribute("GV").equals("F"))
+            else if ( status == GVstatus.F )
                 counter.nRefNotCalled = 1L;
             else
                 counter.nNoStatusNotCalled = 1L;
@@ -427,10 +426,11 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
 //            if (!vcComp.hasExtendedAttribute("GV"))
 //                throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
 
+            final GVstatus status = getGVstatus(vcComp);
             if (call.isCalledAlt(callConf)) {
-                if (vcComp.getAttribute("GV").equals("T"))
+                if ( status == GVstatus.T )
                     counter.nAltCalledAlt = 1L;
-                else if (vcComp.getAttribute("GV").equals("F")) {
+                else if ( status == GVstatus.F ) {
                     counter.nRefCalledAlt = 1L;
                     if ( printInterestingSites )
                         System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
@@ -439,12 +439,12 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
                     counter.nNoStatusCalledAlt = 1L;
             }
             else if (call.isCalledRef(callConf)) {
-                if (vcComp.getAttribute("GV").equals("T")) {
+                if ( status == GVstatus.T ) {
                     counter.nAltCalledRef = 1L;
                     if ( printInterestingSites )
                         System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
                 }
-                else if (vcComp.getAttribute("GV").equals("F"))
+                else if ( status == GVstatus.F )
                     counter.nRefCalledRef = 1L;
 
                 else
@@ -452,9 +452,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
             }
             else {
                 counter.nNotConfidentCalls = 1L;
-                if (vcComp.getAttribute("GV").equals("T"))
+                if ( status == GVstatus.T )
                     counter.nAltNotCalled = 1L;
-                else if (vcComp.getAttribute("GV").equals("F"))
+                else if ( status == GVstatus.F )
                     counter.nRefNotCalled = 1L;
                 else
                     counter.nNoStatusNotCalled = 1L;
@@ -475,6 +475,10 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
         return counter;
     }
 
+    private GVstatus getGVstatus(final VariantContext vc) {
+        return ( !vc.hasAttribute("GV") ) ? GVstatus.NONE : (vc.getAttribute("GV").equals("T") ? GVstatus.T : GVstatus.F);
+    }
+
     //---------------------------------------------------------------------------------------------------------------
     //
     // reduce
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index c7b1d0fc7..d1b7cb96f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -459,7 +459,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
             UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
             UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-            UAC.NO_SLOD = true;
             UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
             headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index c92551a73..3e6ab050a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -46,16 +46,20 @@ import java.util.Set;
 
 
 /**
- * Strictly validates a variants file.
+ * Validates a VCF file with an extra strict set of criteria.
  *
  * <p>
  * ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it.
- * Checks include the correctness of the reference base(s), accuracy of AC & AN values, tests against rsIDs
- * when a dbSNP file is provided, and that all alternate alleles are present in at least one sample.
+ * In addition to standard adherence to the VCF specification, this tool performs extra checks to make ensure
+ * the information contained within the file is correct.  Checks include the correctness of the reference base(s),
+ * accuracy of AC & AN values, tests against rsIDs when a dbSNP file is provided, and that all alternate alleles
+ * are present in at least one sample.
+ *
+ * If you are looking simply to test the adherence to the VCF specification, use --validationType NONE.
  *
  * <h2>Input</h2>
  * <p>
- * A variant set to filter.
+ * A variant set to validate.
  * </p>
  *
  * <h2>Examples</h2>
@@ -79,10 +83,9 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
 
     public enum ValidationType {
-        ALL, REF, IDS, ALLELES, CHR_COUNTS
+        ALL, REF, IDS, ALLELES, CHR_COUNTS, NONE
     }
 
-    @Hidden
     @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false)
     protected ValidationType type = ValidationType.ALL;
 
@@ -172,7 +175,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
                 numErrors++;
                 logger.warn("***** " + e.getMessage() + " *****");
             } else {
-                throw new UserException.MalformedFile(file, e.getMessage());
+                throw new UserException.FailsStrictValidation(file, e.getMessage());
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 5f80f77a4..059e9c5fb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -160,7 +160,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
 
                         Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
                         alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
-                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
+                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
                         hapmap.setActualAlleles(alleleMap);
 
                         // also, use the correct positioning for insertions
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 368cb3d11..2226c6458 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -346,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
 
         @Override
         protected String getFreezeFields() {
-            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%n");
+            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%nif (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))%n");
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java b/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java
index 8964c16cb..4455666e8 100644
--- a/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java
+++ b/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java
@@ -4,12 +4,21 @@ package org.broadinstitute.sting.utils;
  * Simple utility class that makes it convenient to print unit adjusted times
  */
 public class AutoFormattingTime {
-    double timeInSeconds;           // in Seconds
-    int precision;      // for format
+    private final int width; // for format
+    private final int precision;      // for format
 
-    public AutoFormattingTime(double timeInSeconds, int precision) {
+    double timeInSeconds;           // in Seconds
+    private final String formatString;
+
+    public AutoFormattingTime(double timeInSeconds, final int width, int precision) {
+        this.width = width;
         this.timeInSeconds = timeInSeconds;
         this.precision = precision;
+        this.formatString = "%" + width + "." + precision + "f %s";
+    }
+
+    public AutoFormattingTime(double timeInSeconds, int precision) {
+        this(timeInSeconds, 6, precision);
     }
 
     public AutoFormattingTime(double timeInSeconds) {
@@ -20,6 +29,20 @@ public class AutoFormattingTime {
         return timeInSeconds;
     }
 
+    /**
+     * @return the precision (a la format's %WIDTH.PERCISIONf)
+     */
+    public int getWidth() {
+        return width;
+    }
+
+    /**
+     * @return the precision (a la format's %WIDTH.PERCISIONf)
+     */
+    public int getPrecision() {
+        return precision;
+    }
+
     /**
      * Instead of 10000 s, returns 2.8 hours
      * @return
@@ -48,6 +71,6 @@ public class AutoFormattingTime {
             }
         }
 
-        return String.format("%6."+precision+"f %s", unitTime, unit);
+        return String.format(formatString, unitTime, unit);
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
index 2663e848f..44a3e9af3 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
@@ -159,6 +159,7 @@ public class VCFHeader {
      */
     public void addMetaDataLine(VCFHeaderLine headerLine) {
         mMetaData.add(headerLine);
+        loadMetaDataMaps();
     }
 
     /**
@@ -236,7 +237,6 @@ public class VCFHeader {
                     + VCFConstants.GENOTYPE_PL_KEY + " field.  As the GATK now only manages PL fields internally"
                     + " automatically adding a corresponding PL field to your VCF header");
             addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
-            loadMetaDataMaps();
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
index 6fda0245b..63927ac84 100644
--- a/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
@@ -99,9 +99,7 @@ public class LoggingNestedIntegerArray<T> extends NestedIntegerArray<T> {
     }
 
     @Override
-    public void put( final T value, final int... keys ) {
-        super.put(value, keys);
-
+    public boolean put( final T value, final int... keys ) {
         StringBuilder logEntry = new StringBuilder();
 
         logEntry.append(logEntryLabel);
@@ -116,5 +114,7 @@ public class LoggingNestedIntegerArray<T> extends NestedIntegerArray<T> {
 
         // PrintStream methods all use synchronized blocks internally, so our logging is thread-safe
         log.println(logEntry.toString());
+
+        return super.put(value, keys);
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java b/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java
index 31d316555..050ed52ac 100755
--- a/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java
@@ -25,9 +25,11 @@
 
 package org.broadinstitute.sting.utils.collections;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -38,18 +40,51 @@ import java.util.List;
 
 public class NestedIntegerArray<T> {
 
+    private static Logger logger = Logger.getLogger(NestedIntegerArray.class);
+
     protected final Object[] data;
 
     protected final int numDimensions;
     protected final int[] dimensions;
 
+    // Preallocate the first two dimensions to limit contention during tree traversals in put()
+    private static final int NUM_DIMENSIONS_TO_PREALLOCATE = 2;
+
     public NestedIntegerArray(final int... dimensions) {
         numDimensions = dimensions.length;
         if ( numDimensions == 0 )
             throw new ReviewedStingException("There must be at least one dimension to an NestedIntegerArray");
         this.dimensions = dimensions.clone();
 
+        int dimensionsToPreallocate = Math.min(dimensions.length, NUM_DIMENSIONS_TO_PREALLOCATE);
+
+        logger.info(String.format("Creating NestedIntegerArray with dimensions %s", Arrays.toString(dimensions)));
+        logger.info(String.format("Pre-allocating first %d dimensions", dimensionsToPreallocate));
+
         data = new Object[dimensions[0]];
+        preallocateArray(data, 0, dimensionsToPreallocate);
+
+        logger.info(String.format("Done pre-allocating first %d dimensions", dimensionsToPreallocate));
+    }
+
+    /**
+     * Recursively allocate the first dimensionsToPreallocate dimensions of the tree
+     *
+     * Pre-allocating the first few dimensions helps limit contention during tree traversals in put()
+     *
+     * @param subarray current node in the tree
+     * @param dimension current level in the tree
+     * @param dimensionsToPreallocate preallocate only this many dimensions (starting from the first)
+     */
+    private void preallocateArray( Object[] subarray, int dimension, int dimensionsToPreallocate ) {
+        if ( dimension >= dimensionsToPreallocate - 1 ) {
+            return;
+        }
+
+        for ( int i = 0; i < subarray.length; i++ ) {
+            subarray[i] = new Object[dimensions[dimension + 1]];
+            preallocateArray((Object[])subarray[i], dimension + 1, dimensionsToPreallocate);
+        }
     }
 
     public T get(final int... keys) {
@@ -59,14 +94,30 @@ public class NestedIntegerArray<T> {
         for( int i = 0; i < numNestedDimensions; i++ ) {
             if ( keys[i] >= dimensions[i] )
                 return null;
+
             myData = (Object[])myData[keys[i]];
             if ( myData == null )
                 return null;
         }
+
         return (T)myData[keys[numNestedDimensions]];
     }
 
-    public synchronized void put(final T value, final int... keys) { // WARNING! value comes before the keys!
+    /**
+     * Insert a value at the position specified by the given keys.
+     *
+     * This method is thread-safe, however the caller MUST check the
+     * return value to see if the put succeeded. This method RETURNS FALSE if
+     * the value could not be inserted because there already was a value present
+     * at the specified location. In this case the caller should do a get() to get
+     * the already-existing value and (potentially) update it.
+     *
+     * @param value value to insert
+     * @param keys keys specifying the location of the value in the tree
+     * @return true if the value was inserted, false if it could not be inserted because there was already
+     *         a value at the specified position
+     */
+    public boolean put(final T value, final int... keys) { // WARNING! value comes before the keys!
         if ( keys.length != numDimensions )
             throw new ReviewedStingException("Exactly " + numDimensions + " keys should be passed to this NestedIntegerArray but " + keys.length + " were provided");
 
@@ -75,15 +126,35 @@ public class NestedIntegerArray<T> {
         for ( int i = 0; i < numNestedDimensions; i++ ) {
             if ( keys[i] >= dimensions[i] )
                 throw new ReviewedStingException("Key " + keys[i] + " is too large for dimension " + i + " (max is " + (dimensions[i]-1) + ")");
-            Object[] temp = (Object[])myData[keys[i]];
-            if ( temp == null ) {
-                temp = new Object[dimensions[i+1]];
-                myData[keys[i]] = temp;
+
+            // If we're at or beyond the last dimension that was pre-allocated, we need to do a synchronized
+            // check to see if the next branch exists, and if it doesn't, create it
+            if ( i >= NUM_DIMENSIONS_TO_PREALLOCATE - 1 ) {
+                synchronized ( myData ) {
+                    if ( myData[keys[i]] == null ) {
+                        myData[keys[i]] = new Object[dimensions[i + 1]];
+                    }
+                }
             }
-            myData = temp;
+
+            myData = (Object[])myData[keys[i]];
         }
 
-        myData[keys[numNestedDimensions]] = value;
+        synchronized ( myData ) {   // lock the bottom row while we examine and (potentially) update it
+
+            // Insert the new value only if there still isn't any existing value in this position
+            if ( myData[keys[numNestedDimensions]] == null ) {
+                myData[keys[numNestedDimensions]] = value;
+            }
+            else {
+                // Already have a value for this leaf (perhaps another thread came along and inserted one
+                // while we traversed the tree), so return false to notify the caller that we didn't put
+                // the item
+                return false;
+            }
+        }
+
+        return true;
     }
 
     public List<T> getAllValues() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index c1f408bc7..a49a12292 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -283,6 +283,12 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class FailsStrictValidation extends UserException {
+        public FailsStrictValidation(File f, String message) {
+            super(String.format("File %s fails strict validation: %s", f.getAbsolutePath(), message));
+        }
+    }
+
     public static class MalformedFile extends UserException {
         public MalformedFile(String message) {
             super(String.format("Unknown file is malformed: %s", message));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
similarity index 72%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
rename to public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index a83adc275..22d249240 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -22,26 +22,29 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.gatk.walkers.genotyper;
+package org.broadinstitute.sting.utils.genotyper;
 
 
-//import org.broadinstitute.sting.gatk.walkers.Requires;
-import com.google.java.contract.Requires;
+import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.io.PrintStream;
+import java.lang.reflect.Constructor;
 import java.util.*;
 
-public class PerReadAlleleLikelihoodMap {
+public abstract class PerReadAlleleLikelihoodMap {
+
     public static final double INDEL_LIKELIHOOD_THRESH = 0.1;
 
-    private List<Allele> alleles;
-    private Map<GATKSAMRecord,Map<Allele,Double>> likelihoodReadMap;
-    public PerReadAlleleLikelihoodMap() {
-        likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
-        alleles = new ArrayList<Allele>();
-    }
+    protected List<Allele> alleles;
+    protected Map<GATKSAMRecord,Map<Allele,Double>> likelihoodReadMap;
+
+    public abstract void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log);
+    public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log);
 
     public void add(GATKSAMRecord read, Allele a, Double likelihood) {
         Map<Allele,Double> likelihoodMap;
@@ -95,16 +98,6 @@ public class PerReadAlleleLikelihoodMap {
     public int getNumberOfStoredElements() {
         return likelihoodReadMap.size();
     }
-    /**
-     * Returns list of reads greedily associated with a particular allele.
-     * Needs to loop for each read, and assign to each allele
-     * @param a                          Desired allele
-     * @return
-     */
-    @Requires("a!=null")
-    public List<GATKSAMRecord> getReadsAssociatedWithAllele(Allele a) {
-        return null;
-    }
 
     public Map<Allele,Double> getLikelihoodsAssociatedWithPileupElement(PileupElement p) {
         if (!likelihoodReadMap.containsKey(p.getRead()))
@@ -129,4 +122,16 @@ public class PerReadAlleleLikelihoodMap {
         }
         return (maxLike - prevMaxLike > INDEL_LIKELIHOOD_THRESH ? mostLikelyAllele : Allele.NO_CALL );
     }
- }
+
+    public static PerReadAlleleLikelihoodMap getBestAvailablePerReadAlleleLikelihoodMap() {
+        final Class PerReadAlleleLikelihoodMapClass = GATKLiteUtils.getProtectedClassIfAvailable(PerReadAlleleLikelihoodMap.class);
+        try {
+            Constructor constructor = PerReadAlleleLikelihoodMapClass.getDeclaredConstructor((Class[])null);
+            constructor.setAccessible(true);
+            return (PerReadAlleleLikelihoodMap)constructor.newInstance();
+        }
+        catch (Exception e) {
+            throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + PerReadAlleleLikelihoodMapClass.getSimpleName());
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
new file mode 100644
index 000000000..7db818592
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+package org.broadinstitute.sting.utils.genotyper;
+
+
+import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.io.PrintStream;
+import java.util.*;
+
+public class StandardPerReadAlleleLikelihoodMap extends PerReadAlleleLikelihoodMap implements PublicPackageSource {
+
+    public StandardPerReadAlleleLikelihoodMap() {
+        likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
+        alleles = new ArrayList<Allele>();
+    }
+
+    // not implemented in the standard version
+    public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {}
+    public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { return pileup; }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java b/public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
index 69cf52fc2..a8715e242 100755
--- a/public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.utils.progressmeter;
 
+import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.*;
@@ -200,6 +201,14 @@ public class ProgressMeter {
                 "Location", processingUnitName, processingUnitName));
     }
 
+    /**
+     * @return the current runtime in nanoseconds
+     */
+    @Ensures("result >= 0")
+    public long getRuntimeInNanoseconds() {
+        return timer.getElapsedTimeNano();
+    }
+
     /**
      * Utility routine that prints out process information (including timing) every N records or
      * every M seconds, for N and M set in global variables.
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
index 7ad9302a8..5d4020a07 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -61,17 +61,6 @@ public class BaseRecalibration {
 //            qualityScoreByFullCovariateKey[i] = new NestedHashMap();
 //    }
 
-    /**
-     * Thread local cache to allow multi-threaded use of this class
-     */
-    private ThreadLocal<ReadCovariates> readCovariatesCache;
-    {
-        readCovariatesCache = new ThreadLocal<ReadCovariates> () {
-            @Override protected ReadCovariates initialValue() {
-                return new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
-            }
-        };
-    }
 
     /**
      * Constructor using a GATK Report file
@@ -113,13 +102,7 @@ public class BaseRecalibration {
             }
         }
 
-        // Compute all covariates for the read
-        // TODO -- the need to clear here suggests there's an error in the indexing / assumption code
-        // TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads?
-        // TODO -- the output varies with -nt 1 and -nt 2 if you don't call clear here
-        // TODO -- needs to be fixed.
-        final ReadCovariates readCovariates = readCovariatesCache.get().clear();
-        RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
+        final ReadCovariates readCovariates = RecalUtils.computeCovariates(read, requestedCovariates);
 
         for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
             if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
index 85568dac9..29c15adf7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
@@ -66,7 +66,9 @@ public class ReadGroupCovariate implements RequiredCovariate {
     }
 
     @Override
-    public String formatKey(final int key) {
+    public synchronized String formatKey(final int key) {
+        // This method is synchronized so that we don't attempt to do a get()
+        // from the reverse lookup table while that table is being updated
         return readGroupReverseLookupTable.get(key);
     }
 
@@ -76,17 +78,32 @@ public class ReadGroupCovariate implements RequiredCovariate {
     }
 
     private int keyForReadGroup(final String readGroupId) {
-        if (!readGroupLookupTable.containsKey(readGroupId)) {
-            readGroupLookupTable.put(readGroupId, nextId);
-            readGroupReverseLookupTable.put(nextId, readGroupId);
-            nextId++;
+        // Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
+        // synchronize only the table updates.
+
+        // Before entering the synchronized block, check to see if this read group is not in our tables.
+        // If it's not, either we will have to insert it, OR another thread will insert it first.
+        // This preliminary check avoids doing any synchronization most of the time.
+        if ( ! readGroupLookupTable.containsKey(readGroupId) ) {
+
+            synchronized ( this ) {
+
+                // Now we need to make sure the key is STILL not there, since another thread may have come along
+                // and inserted it while we were waiting to enter this synchronized block!
+                if ( ! readGroupLookupTable.containsKey(readGroupId) ) {
+                    readGroupLookupTable.put(readGroupId, nextId);
+                    readGroupReverseLookupTable.put(nextId, readGroupId);
+                    nextId++;
+                }
+            }
         }
 
         return readGroupLookupTable.get(readGroupId);
     }
 
     @Override
-    public int maximumKeyValue() {
+    public synchronized int maximumKeyValue() {
+        // Synchronized so that we don't query table size while the tables are being updated
         return readGroupLookupTable.size() - 1;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java b/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java
new file mode 100644
index 000000000..cc50152ac
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.threading;
+
+import java.lang.reflect.Array;
+
+/**
+ * ThreadLocal implementation for arrays
+ *
+ * Example usage:
+ *
+ * private ThreadLocal<byte[]> threadLocalByteArray = new ThreadLocalArray<byte[]>(length, byte.class);
+ * ....
+ * byte[] byteArray = threadLocalByteArray.get();
+ *
+ * @param <T> the type of the array itself (eg., int[], double[], etc.)
+ *
+ * @author David Roazen
+ */
+public class ThreadLocalArray<T> extends ThreadLocal<T> {
+    private int arraySize;
+    private Class arrayElementType;
+
+    /**
+     * Create a new ThreadLocalArray
+     *
+     * @param arraySize desired length of the array
+     * @param arrayElementType type of the elements within the array (eg., Byte.class, Integer.class, etc.)
+     */
+    public ThreadLocalArray( int arraySize, Class arrayElementType ) {
+        super();
+
+        this.arraySize = arraySize;
+        this.arrayElementType = arrayElementType;
+    }
+
+    @Override
+    @SuppressWarnings("unchecked")
+    protected T initialValue() {
+        return (T)Array.newInstance(arrayElementType, arraySize);
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index e453e2f8a..27a5b0c24 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1071,15 +1071,17 @@ public class VariantContext implements Feature { // to enable tribble integratio
             if ( g.isCalled() )
                 observedAlleles.addAll(g.getAlleles());
         }
+        if ( observedAlleles.contains(Allele.NO_CALL) )
+            observedAlleles.remove(Allele.NO_CALL);
 
         if ( reportedAlleles.size() != observedAlleles.size() )
-            throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart()));
+            throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getChr(), getStart()));
 
         int originalSize = reportedAlleles.size();
         // take the intersection and see if things change
         observedAlleles.retainAll(reportedAlleles);
         if ( observedAlleles.size() != originalSize )
-            throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart()));
+            throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getChr(), getStart()));
     }
 
     public void validateChromosomeCounts() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index 913615a84..abe85e383 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -193,6 +193,8 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
                 infoMap.put("isHet", g.isHet() ? "1" : "0");
                 infoMap.put("isHomVar", g.isHomVar() ? "1" : "0");
                 infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getGQ());
+                if ( g.hasDP() )
+                    infoMap.put(VCFConstants.DEPTH_KEY, g.getDP());
                 for ( Map.Entry<String, Object> e : g.getExtendedAttributes().entrySet() ) {
                     if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) )
                         infoMap.put(e.getKey(), e.getValue());
diff --git a/public/java/test/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java
new file mode 100644
index 000000000..6cfd7bf46
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.SimpleTimer;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.concurrent.TimeUnit;
+
+/**
+ *
+ */
+public class MaxRuntimeIntegrationTest extends WalkerTest {
+    private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(20, TimeUnit.SECONDS);
+
+    private class MaxRuntimeTestProvider extends TestDataProvider {
+        final long maxRuntime;
+        final TimeUnit unit;
+
+        public MaxRuntimeTestProvider(final long maxRuntime, final TimeUnit unit) {
+            super(MaxRuntimeTestProvider.class);
+            this.maxRuntime = maxRuntime;
+            this.unit = unit;
+            setName(String.format("Max runtime test : %d of %s", maxRuntime, unit));
+        }
+
+        public long expectedMaxRuntimeNano() {
+            return TimeUnit.NANOSECONDS.convert(maxRuntime, unit) + STARTUP_TIME;
+        }
+    }
+
+    @DataProvider(name = "MaxRuntimeProvider")
+    public Object[][] makeMaxRuntimeProvider() {
+        for ( final TimeUnit requestedUnits : Arrays.asList(TimeUnit.NANOSECONDS, TimeUnit.MILLISECONDS, TimeUnit.SECONDS, TimeUnit.MINUTES) )
+            new MaxRuntimeTestProvider(requestedUnits.convert(30, TimeUnit.SECONDS), requestedUnits);
+
+        return MaxRuntimeTestProvider.getTests(MaxRuntimeTestProvider.class);
+    }
+
+    //
+    // Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
+    //
+    @Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
+    public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + hg18Reference
+                        + " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null"
+                        + " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0,
+                Collections.<String>emptyList());
+        final SimpleTimer timer = new SimpleTimer().start();
+        executeTest("Max runtime " + cfg, spec);
+        final long actualRuntimeNano = timer.getElapsedTimeNano();
+
+        Assert.assertTrue(actualRuntimeNano < cfg.expectedMaxRuntimeNano(),
+                "Actual runtime " + TimeUnit.SECONDS.convert(actualRuntimeNano, TimeUnit.NANOSECONDS)
+                        + " exceeded max. tolerated runtime " + TimeUnit.SECONDS.convert(cfg.expectedMaxRuntimeNano(), TimeUnit.NANOSECONDS)
+                        + " given requested runtime " + cfg.maxRuntime + " " + cfg.unit);
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 97b985a29..27e5f3d46 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -108,4 +108,22 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
                 Arrays.asList("8ed32a2272bab8043a255362335395ef"));
         executeTest("testUnfilteredBecomesFilteredAndPass", spec);
     }
+
+    @Test
+    public void testFilteringDPfromINFO() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+                        + " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
+                Arrays.asList("a01f7cce53ea556c9741aa60b6124c41"));
+        executeTest("testFilteringDPfromINFO", spec);
+    }
+
+    @Test
+    public void testFilteringDPfromFORMAT() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+                        + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
+                Arrays.asList("e10485c7c33d9211d0c1294fd7858476"));
+        executeTest("testFilteringDPfromFORMAT", spec);
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index dee54b9f8..9212d0e53 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -16,9 +16,9 @@ import java.util.List;
 
 public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
-    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
-    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
-    private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
+    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
+    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
+    private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
     private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
 
     // --------------------------------------------------------------------------------------------------------------
@@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("847605f4efafef89529fe0e496315edd"));
+                Arrays.asList("cdec335abc9ad8e59335e39a73e0e95a"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -38,7 +38,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("bc15123620e1134f799005d71d1180fe"));
+                Arrays.asList("efddb5e258f97fd4f6661cff9eaa57de"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
     }
 
@@ -46,7 +46,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("1ba7afccc8552f20d72d0b62237558e3"));
+                Arrays.asList("24532eb381724cd74e99370da28d49ed"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -54,22 +54,22 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("afb8768f31ab57eb43f75c1115eadc99"));
+                Arrays.asList("062a946160eec1d0fc135d58ca654ff4"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
     @Test
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("543f68e42034bf44cfb24da8c9204320"));
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
+                Arrays.asList("94dc17d76d841f1d3a36160767ffa034"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
     @Test
     public void testBadRead() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
                 Arrays.asList("d915535c1458733f09f82670092fcab6"));
         executeTest("test bad read", spec);
     }
@@ -77,16 +77,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("5ce03dd9ca2d9324c1d4a9d64389beb5"));
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
+                Arrays.asList("9106d01ca0d0a8fedd068e72d509f380"));
         executeTest("test reverse trim", spec);
     }
 
     @Test
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("3c006b06b17bbe8e787d64eff6a63a19"));
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
+                Arrays.asList("d847acf841ba8ba653f996ce4869f439"));
         executeTest("test mismatched PLs", spec);
     }
 
@@ -96,7 +96,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "fd236bd635d514e4214d364f45ec4d10";
+    private final static String COMPRESSED_OUTPUT_MD5 = "6792419c482e767a3deb28913ed2b1ad";
 
     @Test
     public void testCompressedOutput() {
@@ -120,21 +120,21 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         String md5 = "d408b4661b820ed86272415b8ea08780";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
+                baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (single thread)", spec1);
 
         GenomeAnalysisEngine.resetRandomGenerator();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
+                baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (2 threads)", spec2);
 
         GenomeAnalysisEngine.resetRandomGenerator();
 
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
+                baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (4 threads)", spec3);
     }
@@ -149,15 +149,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinBaseQualityScore() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
-                Arrays.asList("839ecd30d354a36b5dfa2b5e99859765"));
+                Arrays.asList("56157d930da6ccd224bce1ca93f11e41"));
         executeTest("test min_base_quality_score 26", spec);
     }
 
     @Test
     public void testSLOD() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9"));
+                "-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
+                Arrays.asList("6ccb9bd88934e4272d0ce362dd35e603"));
         executeTest("test SLOD", spec);
     }
 
@@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNDA() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("abd8e33e649cc11b55e200d3940cc7e2"));
+                Arrays.asList("480437dd6e2760f4ab3194431519f331"));
         executeTest("test NDA", spec);
     }
 
@@ -173,7 +173,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testCompTrack() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("8a9b424e00cdbe6b5e73d517335b2186"));
+                Arrays.asList("22c039412fd387dde6125b07c9a74a25"));
         executeTest("test using comp track", spec);
     }
 
@@ -187,17 +187,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testOutputParameterSitesOnly() {
-        testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311");
+        testOutputParameters("-sites_only", "40aeb4c9e31fe7046b72afc58e7599cb");
     }
 
     @Test
     public void testOutputParameterAllConfident() {
-        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
+        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "c706ca93b25ff83613cb4e95dcac567c");
     }
 
     @Test
     public void testOutputParameterAllSites() {
-        testOutputParameters("--output_mode EMIT_ALL_SITES", "41c046d38ea328421df924e37e017645");
+        testOutputParameters("--output_mode EMIT_ALL_SITES", "8a263fd0a94463ce1de9990f2b8ec841");
     }
 
     private void testOutputParameters(final String args, final String md5) {
@@ -211,18 +211,10 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
+                Arrays.asList("df524e98903d96ab9353bee7c16a69de"));
         executeTest("test confidence 1", spec1);
     }
 
-    @Test
-    public void testConfidence2() {
-        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
-        executeTest("test confidence 2", spec2);
-    }
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing heterozygosity
@@ -230,12 +222,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testHeterozyosity1() {
-        testHeterozosity( 0.01, "986923de51c71635d47e3d06fe3794a1" );
+        testHeterozosity( 0.01, "8e61498ca03a8d805372a64c466b3b42" );
     }
 
     @Test
     public void testHeterozyosity2() {
-        testHeterozosity( 1.0 / 1850, "fb12b1553f813004a394a391a8540873" );
+        testHeterozosity( 1.0 / 1850, "668d06b5173cf3b97d052726988e1d7b" );
     }
 
     private void testHeterozosity(final double arg, final String md5) {
@@ -259,7 +251,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("04a87b87ee4323eba853c78f25551d1a"));
+                Arrays.asList("908eb5e21fa39e7fb377cf4a9c4c7835"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -278,7 +270,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("98058fc913b61c22d44875da1f5ea89c"));
+                Arrays.asList("c814558bb0ed2e19b12e1a2bf4465d52"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -297,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("650c53774afacfc07a595675e8cdde17"));
+                Arrays.asList("3593495aab5f6204c65de0b073a6ff65"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -312,7 +304,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("6a0c2a3a7bcc56ad01428c71408055aa"));
+                Arrays.asList("8b486a098029d5a106b0a37eff541c15"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -325,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("5f2721c3323de5390d2d47446139f32b"));
+                 Arrays.asList("18efedc50cae2aacaba372265e38310b"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -335,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("7e3f67bf371112be5dbadb4fe6faa52a"));
+                Arrays.asList("3ff8c7c80a518aa3eb8671a21479de5f"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
     }
 
@@ -345,7 +337,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("bc31c4977cb7e563ddf9c8dea27f3f4f"));
+                Arrays.asList("578c0540f4f2052a634a829bcb9cc27d"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
@@ -353,13 +345,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSampleIndels1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("a4761d7f25e7a62f34494801c98a0da7"));
+                Arrays.asList("f7d0d0aee603df25c1f0525bb8df189e"));
         List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("c526c234947482d1cd2ffc5102083a08"));
+                Arrays.asList("fc91d457a16b4ca994959c2b5f3f0352"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -415,7 +407,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("ba4fafec383fb988f20c8cf53dd3e9a0"));
+                Arrays.asList("857b8e5df444463ac27f665c4f67fbe2"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -423,7 +415,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("4c57a88de275105156aaafc6f9041365"));
+                Arrays.asList("81d4c7d9010fd6733b2997bc378e7471"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 
@@ -444,8 +436,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testNsInCigar() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
-                Arrays.asList("e8ebfaac0804b782f22ab8ea35152735"));
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
+                Arrays.asList("bd7984a374f0ae5d277bd5fc5065f64f"));
         executeTest("test calling on reads with Ns in CIGAR", spec);
     }
 
@@ -458,26 +450,42 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("da9c05f87bd6415e97f90c49cf68ed19"));
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
+                Arrays.asList("9a7cd58b9e3d5b72608c0d529321deba"));
         executeTest("test calling on a ReducedRead BAM", spec);
     }
 
     @Test
     public void testReducedBamSNPs() {
-        testReducedCalling("SNP", "1d4a826b144723ff0766c36aa0239287");
+        testReducedCalling("SNP", "e7fc11baf208a1bca7b462d3148c936e");
     }
 
     @Test
     public void testReducedBamINDELs() {
-        testReducedCalling("INDEL", "68ef51d5c98480e0c0192e0eecb95bca");
+        testReducedCalling("INDEL", "132a4e0ccf9230b5bb4b56c649e2bdd5");
     }
 
 
     private void testReducedCalling(final String model, final String md5) {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
                 Arrays.asList(md5));
         executeTest("test calling on a ReducedRead BAM with " + model, spec);
     }
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing contamination down-sampling
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Test
+    public void testContaminationDownsampling() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_fraction_to_filter 0.20", 1,
+                Arrays.asList("27dd04159e06d9524fb8a4eef41f96ae"));
+        executeTest("test contamination_percentage_to_filter 0.20", spec);
+    }
+
+
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index c92d6d4cf..7a3a20bdd 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -354,7 +354,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompOverlap() {
         String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + variantEvalTestDataRoot + "pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + variantEvalTestDataRoot + "pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("59ad39e03678011b5f62492fa83ede04"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d0d9208060e69e157dac3bf01bdd83b0"));
         executeTestParallel("testCompOverlap",spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index aec087f2c..0c4924229 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
-            "f360ce3eb2b0b887301be917a9843e2b",  // tranches
-            "287fea5ea066bf3fdd71f5ce9b58eab3",  // recal file
-            "afa297c743437551cc2bd36ddd6d6d75"); // cut VCF
+            "4d08c8eee61dd1bdea8c5765f34e41f0",  // tranches
+            "ce396fe4045e020b61471f6737dff36e",  // recal file
+            "4f59bd61be900b25c6ecedaa68b9c8de"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -75,9 +75,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
-            "a8ce3cd3dccafdf7d580bcce7d660a9a",  // tranches
-            "74c10fc15f9739a938b7138909fbde04",  // recal file
-            "c30d163871a37f2bbf8ee7f761e870b4"); // cut VCF
+            "6a1eef4d02857dbb117a15420b5c0ce9",  // tranches
+            "238366af66b05b6d21749e799c25353d",  // recal file
+            "3928d6bc5007becf52312ade70f14c42"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
     public Object[][] createVRBCFTest() {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index f29ac8cad..a1d673b56 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -20,7 +20,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("d88bdae45ae0e74e8d8fd196627e612c")
+                Arrays.asList("954415f84996d27b07d00855e96d33a2")
         );
         spec.disableShadowBCF();
 
@@ -49,7 +49,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf")
+                Arrays.asList("ca1b5226eaeaffb78d4abd9d2ee10c43")
         );
         spec.disableShadowBCF();
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
index 6a3d755d7..67d47997b 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
@@ -33,6 +33,8 @@ import java.util.Arrays;
 
 public class ValidateVariantsIntegrationTest extends WalkerTest {
 
+    protected static final String emptyMd5 = "d41d8cd98f00b204e9800998ecf8427e";
+
     public static String baseTestString(String file, String type) {
         return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + privateTestDir + file + " --validationType " + type;
     }
@@ -42,7 +44,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleGood.vcf", "ALL"),
                 0,
-                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")
+                Arrays.asList(emptyMd5)
         );
 
         executeTest("test good file", spec);
@@ -53,7 +55,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad.vcf", "REF"),
                 0,
-                UserException.MalformedFile.class
+                UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad ref base #1", spec);
@@ -64,7 +66,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad2.vcf", "REF"),
                 0,
-                UserException.MalformedFile.class
+                UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad ref base #2", spec);
@@ -75,7 +77,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad.vcf", "CHR_COUNTS"),
                 0,
-                UserException.MalformedFile.class
+                UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad chr counts #1", spec);
@@ -86,7 +88,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad2.vcf", "CHR_COUNTS"),
                 0,
-                UserException.MalformedFile.class
+                UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad chr counts #2", spec);
@@ -97,7 +99,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad.vcf", "IDS") + " --dbsnp " + b36dbSNP129,
                 0,
-                UserException.MalformedFile.class
+                UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad RS ID", spec);
@@ -108,7 +110,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             baseTestString("validationExampleBad.vcf", "ALLELES"),
             0,
-            UserException.MalformedFile.class
+            UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad alt allele", spec);
@@ -119,18 +121,29 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             baseTestString("validationExampleBad3.vcf", "REF"),
             0,
-            UserException.MalformedFile.class
+            UserException.FailsStrictValidation.class
         );
 
         executeTest("test bad ref allele in deletion", spec);
     }
 
+    @Test
+    public void testNoValidation() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("validationExampleBad.vcf", "NONE"),
+                0,
+                Arrays.asList(emptyMd5)
+        );
+
+        executeTest("test no validation", spec);
+    }
+
     @Test
     public void testComplexEvents() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("complexEvents.vcf", "ALL"),
                 0,
-                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")
+                Arrays.asList(emptyMd5)
         );
 
         executeTest("test validating complex events", spec);
diff --git a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
index 37614f15f..80b0b4ee2 100755
--- a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
@@ -32,11 +32,12 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(
                         "-T UnifiedGenotyper -R " + b37KGReference,
-                        "-nosl --no_cmdline_in_header -G",
+                        "--no_cmdline_in_header -G",
                         //"--dbsnp " + b37dbSNP132,
                         "-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam",
                         "-L 20:10,000,000-10,100,000",
                         "-glm " + glm,
+                        "--contamination_fraction_to_filter 0.0",
                         "-nt " + nt,
                         "-nct " + nct,
                         "-o %s"
diff --git a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java
index 2ba2da734..af2e18ad9 100644
--- a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java
@@ -23,6 +23,7 @@ import java.util.List;
  * To change this template use File | Settings | File Templates.
  */
 public class NanoSchedulerUnitTest extends BaseTest {
+    private final static boolean DEBUG = false;
     private final static boolean debug = false;
     public static final int NANO_SCHEDULE_MAX_RUNTIME = 30000;
 
@@ -30,19 +31,22 @@ public class NanoSchedulerUnitTest extends BaseTest {
         @Override public Integer apply(Integer input) { return input * 2; }
     }
 
+    private static void maybeDelayMe(final int input) {
+        try {
+            if ( input % 7 == 0 ) {
+                final int milliToSleep = (input % 10);
+                //System.out.printf("Sleeping %d millseconds%n", milliToSleep);
+                Thread.sleep(milliToSleep);
+            }
+        } catch ( InterruptedException ex ) {
+            throw new RuntimeException(ex);
+        }
+    }
+
     private static class Map2xWithDelays extends Map2x {
         @Override public Integer apply(Integer input) {
-            try {
-                if ( input % 7 == 0 ) {
-                    final int milliToSleep = (input % 10);
-                    //System.out.printf("Sleeping %d millseconds%n", milliToSleep);
-                    Thread.sleep(milliToSleep);
-                }
-
-                return input * 2;
-            } catch ( InterruptedException ex ) {
-                throw new RuntimeException(ex);
-            }
+            maybeDelayMe(input);
+            return input * 2;
         }
     }
 
@@ -117,10 +121,12 @@ public class NanoSchedulerUnitTest extends BaseTest {
     }
 
     static NanoSchedulerBasicTest exampleTest = null;
+    static NanoSchedulerBasicTest exampleTestWithDelays = null;
 
     @BeforeSuite
     public void setUp() throws Exception {
         exampleTest = new NanoSchedulerBasicTest(10, 2, 1, 10, false);
+        exampleTestWithDelays = new NanoSchedulerBasicTest(10, 2, 1, 10, true);
     }
 
     @DataProvider(name = "NanoSchedulerBasicTest")
@@ -151,14 +157,14 @@ public class NanoSchedulerUnitTest extends BaseTest {
         return NanoSchedulerBasicTest.getTests(NanoSchedulerBasicTest.class);
     }
 
-    @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME)
+    @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME)
     public void testSingleThreadedNanoScheduler(final NanoSchedulerBasicTest test) throws InterruptedException {
         logger.warn("Running " + test);
         if ( test.nThreads == 1 )
             testNanoScheduler(test);
     }
 
-    @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME, dependsOnMethods = "testSingleThreadedNanoScheduler")
+    @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", timeOut = NANO_SCHEDULE_MAX_RUNTIME, dependsOnMethods = "testSingleThreadedNanoScheduler")
     public void testMultiThreadedNanoScheduler(final NanoSchedulerBasicTest test) throws InterruptedException {
         logger.warn("Running " + test);
         if ( test.nThreads >= 1 )
@@ -195,7 +201,7 @@ public class NanoSchedulerUnitTest extends BaseTest {
         }
     }
 
-    @Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", dependsOnMethods = "testMultiThreadedNanoScheduler", timeOut = NANO_SCHEDULE_MAX_RUNTIME)
+    @Test(enabled = true && ! DEBUG, dataProvider = "NanoSchedulerBasicTest", dependsOnMethods = "testMultiThreadedNanoScheduler", timeOut = NANO_SCHEDULE_MAX_RUNTIME)
     public void testNanoSchedulerInLoop(final NanoSchedulerBasicTest test) throws InterruptedException {
         if ( test.bufferSize > 1) {
             logger.warn("Running " + test);
@@ -213,7 +219,7 @@ public class NanoSchedulerUnitTest extends BaseTest {
         }
     }
 
-    @Test(timeOut = NANO_SCHEDULE_MAX_RUNTIME)
+    @Test(enabled = true && ! DEBUG, timeOut = NANO_SCHEDULE_MAX_RUNTIME)
     public void testShutdown() throws InterruptedException {
         final NanoScheduler<Integer, Integer, Integer> nanoScheduler = new NanoScheduler<Integer, Integer, Integer>(1, 2);
         Assert.assertFalse(nanoScheduler.isShutdown(), "scheduler should be alive");
@@ -221,38 +227,78 @@ public class NanoSchedulerUnitTest extends BaseTest {
         Assert.assertTrue(nanoScheduler.isShutdown(), "scheduler should be dead");
     }
 
-    @Test(expectedExceptions = IllegalStateException.class, timeOut = NANO_SCHEDULE_MAX_RUNTIME)
+    @Test(enabled = true && ! DEBUG, expectedExceptions = IllegalStateException.class, timeOut = NANO_SCHEDULE_MAX_RUNTIME)
     public void testShutdownExecuteFailure() throws InterruptedException {
         final NanoScheduler<Integer, Integer, Integer> nanoScheduler = new NanoScheduler<Integer, Integer, Integer>(1, 2);
         nanoScheduler.shutdown();
         nanoScheduler.execute(exampleTest.makeReader(), exampleTest.makeMap(), exampleTest.initReduce(), exampleTest.makeReduce());
     }
 
-    @Test(expectedExceptions = NullPointerException.class, timeOut = 10000, invocationCount = 50)
+    @DataProvider(name = "NanoSchedulerInputExceptionTest")
+    public Object[][] createNanoSchedulerInputExceptionTest() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+
+        for ( final int bufSize : Arrays.asList(100) ) {
+            for ( final int nThreads : Arrays.asList(8) ) {
+                for ( final boolean addDelays : Arrays.asList(true, false) ) {
+                    final NanoSchedulerBasicTest test = new NanoSchedulerBasicTest(bufSize, nThreads, 1, 1000000, false);
+                    final int maxN = addDelays ? 10000 : 100000;
+                    for ( int nElementsBeforeError = 0; nElementsBeforeError < maxN; nElementsBeforeError += Math.max(nElementsBeforeError / 10, 1) ) {
+                        tests.add(new Object[]{nElementsBeforeError, test, addDelays});
+                    }
+                }
+            }
+        }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(enabled = true, expectedExceptions = NullPointerException.class, timeOut = 10000)
     public void testInputErrorIsThrown_NPE() throws InterruptedException {
-        executeTestErrorThrowingInput(new NullPointerException());
+        executeTestErrorThrowingInput(10, new NullPointerException(), exampleTest, false);
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class, timeOut = 10000, invocationCount = 50)
+    @Test(enabled = true, expectedExceptions = ReviewedStingException.class, timeOut = 10000)
     public void testInputErrorIsThrown_RSE() throws InterruptedException {
-        executeTestErrorThrowingInput(new ReviewedStingException("test"));
+        executeTestErrorThrowingInput(10, new ReviewedStingException("test"), exampleTest, false);
     }
 
-    private void executeTestErrorThrowingInput(final RuntimeException ex) {
-        final NanoScheduler<Integer, Integer, Integer> nanoScheduler = new NanoScheduler<Integer, Integer, Integer>(1, 2);
-        nanoScheduler.execute(new ErrorThrowingIterator(ex), exampleTest.makeMap(), exampleTest.initReduce(), exampleTest.makeReduce());
+    @Test(enabled = true, expectedExceptions = NullPointerException.class, dataProvider = "NanoSchedulerInputExceptionTest", timeOut = 10000, invocationCount = 1)
+    public void testInputErrorDoesntDeadlock(final int nElementsBeforeError, final NanoSchedulerBasicTest test, final boolean addDelays ) throws InterruptedException {
+        executeTestErrorThrowingInput(nElementsBeforeError, new NullPointerException(), test, addDelays);
+    }
+
+    private void executeTestErrorThrowingInput(final int nElementsBeforeError, final RuntimeException ex, final NanoSchedulerBasicTest test, final boolean addDelays) {
+        logger.warn("executeTestErrorThrowingInput " + nElementsBeforeError + " ex=" + ex + " test=" + test + " addInputDelays=" + addDelays);
+        final NanoScheduler<Integer, Integer, Integer> nanoScheduler = test.makeScheduler();
+        nanoScheduler.execute(new ErrorThrowingIterator(nElementsBeforeError, ex, addDelays), test.makeMap(), test.initReduce(), test.makeReduce());
     }
 
     private static class ErrorThrowingIterator implements Iterator<Integer> {
+        final int nElementsBeforeError;
+        final boolean addDelays;
+        int i = 0;
         final RuntimeException ex;
 
-        private ErrorThrowingIterator(RuntimeException ex) {
+        private ErrorThrowingIterator(final int nElementsBeforeError, RuntimeException ex, boolean addDelays) {
+            this.nElementsBeforeError = nElementsBeforeError;
             this.ex = ex;
+            this.addDelays = addDelays;
         }
 
-        @Override public boolean hasNext() { throw ex; }
-        @Override public Integer next() { throw ex; }
-        @Override public void remove() { throw ex; }
+        @Override public boolean hasNext() { return true; }
+        @Override public Integer next() {
+            if ( i++ > nElementsBeforeError ) {
+                throw ex;
+            } else if ( addDelays ) {
+                maybeDelayMe(i);
+                return i;
+            } else {
+                return i;
+            }
+        }
+        @Override public void remove() { throw new UnsupportedOperationException("x"); }
     }
 
     public static void main(String [ ] args) {
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 5e66520ca..24ab50451 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -136,7 +136,14 @@ class GATKResourcesBundle extends QScript {
 
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf",
       "Mills_and_1000G_gold_standard.indels", b37, true, false))
-    
+
+    //
+    // CEU trio (NA12878,NA12891,NA12892) best practices results (including PBT)
+    //
+
+    addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/callsets/CEUtrio_BestPractices/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.phased.CURRENT.vcf",
+      "CEUTrio.HiSeq.WGS.b37.bestPractices.phased",b37,true,false))
+
     //
     // example call set for wiki tutorial
     //
@@ -310,6 +317,7 @@ class GATKResourcesBundle extends QScript {
   class UG(@Input bam: File, @Input ref: File, @Input outVCF: File) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
     this.input_file = List(bam)
     this.reference_sequence = ref
+    this.intervalsString ++= List("20");
     this.out = outVCF
   }
 
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
index 19f00ac62..944ef7977 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
@@ -60,7 +60,7 @@ class DataProcessingPipelineTest {
       " -bwa /home/unix/carneiro/bin/bwa",
       " -bwape ",
       " -p " + projectName).mkString
-    spec.fileMD5s += testOut -> "6e70efbe6bafc3fedd60bd406bd201db"
+    spec.fileMD5s += testOut -> "9fca827ecc8436465b831bb6f879357a"
     PipelineTest.executeTest(spec)
   }
 
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
index 74e947377..3e9af3e68 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
@@ -40,7 +40,7 @@ class PacbioProcessingPipelineTest {
       " -blasr ",
       " -test ",
       " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString
-    spec.fileMD5s += testOut -> "61b06e8b78a93e6644657e6d38851084"
+    spec.fileMD5s += testOut -> "b84f9c45e045685067ded681d5e6224c"
     PipelineTest.executeTest(spec)
   }
 }