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 b0043e68c..39e1bdc72 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -15,6 +15,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.Queue;
 import java.util.concurrent.ExecutorService;
@@ -41,7 +42,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
      */
     private ThreadLocalOutputTracker outputTracker = new ThreadLocalOutputTracker();
 
-    private final Queue<Shard> traverseTasks = new LinkedList<Shard>();
     private final Queue<TreeReduceTask> reduceTasks = new LinkedList<TreeReduceTask>();
 
     /**
@@ -49,6 +49,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
      */
     private Throwable error = null;
 
+    /**
+     * Queue of incoming shards.
+     */
+    private Iterator<Shard> traversalTasks;
+
     /**
      * Keep a queue of shard traversals, and constantly monitor it to see what output
      * merge tasks remain.
@@ -56,9 +61,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
      */
     private final Queue<ShardTraverser> outputMergeTasks = new LinkedList<ShardTraverser>();
 
-    /** How many total tasks were in the queue at the start of run. */
-    private int totalTraversals = 0;
-
     /** How many shard traversals have run to date? */
     private int totalCompletedTraversals = 0;
 
@@ -92,13 +94,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         if (!( walker instanceof TreeReducible ))
             throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
 
+        this.traversalTasks = shardStrategy.iterator();
+
         ReduceTree reduceTree = new ReduceTree(this);
         initializeWalker(walker);
 
-        for (Shard shard : shardStrategy)
-            traverseTasks.add(shard);
-        totalTraversals = traverseTasks.size();
-
         while (isShardTraversePending() || isTreeReducePending()) {
             // Check for errors during execution.
             if(hasTraversalErrorOccurred())
@@ -190,7 +190,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
      * @return true if a shard traversal is waiting; false otherwise.
      */
     protected boolean isShardTraversePending() {
-        return traverseTasks.size() > 0;
+        return traversalTasks.hasNext();
     }
 
     /**
@@ -283,10 +283,10 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
      * @param reduceTree Tree of reduces to which to add this shard traverse.
      */
     protected void queueNextShardTraverse( Walker walker, ReduceTree reduceTree ) {
-        if (traverseTasks.size() == 0)
+        if (!traversalTasks.hasNext())
             throw new IllegalStateException("Cannot traverse; no pending traversals exist.");
 
-        Shard shard = traverseTasks.remove();
+        Shard shard = traversalTasks.next();
 
         // todo -- add ownership claim here
 
@@ -398,16 +398,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
 
     }
 
-    /** {@inheritDoc} */
-    public int getTotalNumberOfShards() {
-        return totalTraversals;
-    }
-
-    /** {@inheritDoc} */
-    public int getRemainingNumberOfShards() {
-        return traverseTasks.size();
-    }
-
     /** {@inheritDoc} */
     public int getNumberOfTasksInReduceQueue() {
         return reduceTasks.size();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java
index 21a87963b..530285db0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java
@@ -17,18 +17,6 @@ package org.broadinstitute.sting.gatk.executive;
  * microscheduler is behaving. 
  */
 public interface HierarchicalMicroSchedulerMBean extends MicroSchedulerMBean {
-    /**
-     * What is the total number of shards assigned to this microscheduler?
-     * @return Total number of shards to process.
-     */
-    public int getTotalNumberOfShards();
-
-    /**
-     * How many shards are remaining for this microscheduler to process?
-     * @return Remaining number of shards to process.
-     */
-    public int getRemainingNumberOfShards();
-
     /**
      * How many tree reduces are waiting in the tree reduce queue?
      * @return Total number of reduces waiting in the tree reduce queue?
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 24fd48387..f2e54713f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -43,7 +43,8 @@ import java.util.*;
  * @version 0.1
  */
 public class ReadUtils {
-    private ReadUtils() { }
+    private ReadUtils() {
+    }
 
     private static int DEFAULT_ADAPTOR_SIZE = 100;
 
@@ -57,10 +58,11 @@ public class ReadUtils {
 
     /**
      * A HashMap of the SAM spec read flag names
-     *
+     * <p/>
      * Note: This is not being used right now, but can be useful in the future
      */
     private static final Map<Integer, String> readFlagNames = new HashMap<Integer, String>();
+
     static {
         readFlagNames.put(0x1, "Paired");
         readFlagNames.put(0x2, "Proper");
@@ -77,47 +79,49 @@ public class ReadUtils {
 
     /**
      * This enum represents all the different ways in which a read can overlap an interval.
-     *
+     * <p/>
      * NO_OVERLAP_CONTIG:
      * read and interval are in different contigs.
-     *
+     * <p/>
      * NO_OVERLAP_LEFT:
      * the read does not overlap the interval.
-     *
-     *                        |----------------| (interval)
-     *   <---------------->                      (read)
-     *
+     * <p/>
+     * |----------------| (interval)
+     * <---------------->                      (read)
+     * <p/>
      * NO_OVERLAP_RIGHT:
      * the read does not overlap the interval.
-     *
-     *   |----------------|                      (interval)
-     *                        <----------------> (read)
-     *
+     * <p/>
+     * |----------------|                      (interval)
+     * <----------------> (read)
+     * <p/>
      * OVERLAP_LEFT:
      * the read starts before the beginning of the interval but ends inside of it
-     *
-     *          |----------------| (interval)
-     *   <---------------->        (read)
-     *
+     * <p/>
+     * |----------------| (interval)
+     * <---------------->        (read)
+     * <p/>
      * OVERLAP_RIGHT:
      * the read starts inside the interval but ends outside of it
-     *
-     *   |----------------|     (interval)
-     *       <----------------> (read)
-     *
+     * <p/>
+     * |----------------|     (interval)
+     * <----------------> (read)
+     * <p/>
      * OVERLAP_LEFT_AND_RIGHT:
      * the read starts before the interval and ends after the interval
-     *
-     *      |-----------|     (interval)
-     *  <-------------------> (read)
-     *
+     * <p/>
+     * |-----------|     (interval)
+     * <-------------------> (read)
+     * <p/>
      * OVERLAP_CONTAINED:
      * the read starts and ends inside the interval
-     *
-     *  |----------------|     (interval)
-     *     <-------->          (read)
+     * <p/>
+     * |----------------|     (interval)
+     * <-------->          (read)
      */
-    public enum ReadAndIntervalOverlap {NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT, NO_OVERLAP_RIGHT, NO_OVERLAP_HARDCLIPPED_LEFT, NO_OVERLAP_HARDCLIPPED_RIGHT, OVERLAP_LEFT, OVERLAP_RIGHT, OVERLAP_LEFT_AND_RIGHT, OVERLAP_CONTAINED}
+    public enum ReadAndIntervalOverlap {
+        NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT, NO_OVERLAP_RIGHT, NO_OVERLAP_HARDCLIPPED_LEFT, NO_OVERLAP_HARDCLIPPED_RIGHT, OVERLAP_LEFT, OVERLAP_RIGHT, OVERLAP_LEFT_AND_RIGHT, OVERLAP_CONTAINED
+    }
 
     /**
      * Creates a SAMFileWriter with the given compression level if you request a bam file. Creates a regular
@@ -137,15 +141,15 @@ public class ReadUtils {
 
     /**
      * is this base inside the adaptor of the read?
-     *
+     * <p/>
      * There are two cases to treat here:
-     *
+     * <p/>
      * 1) Read is in the negative strand => Adaptor boundary is on the left tail
      * 2) Read is in the positive strand => Adaptor boundary is on the right tail
-     *
+     * <p/>
      * Note: We return false to all reads that are UNMAPPED or have an weird big insert size (probably due to mismapping or bigger event)
      *
-     * @param read the read to test
+     * @param read    the read to test
      * @param basePos base position in REFERENCE coordinates (not read coordinates)
      * @return whether or not the base is in the adaptor
      */
@@ -162,39 +166,37 @@ public class ReadUtils {
      * the read boundary. If the read is in the positive strand, this is the first base after the end of the
      * fragment (Picard calls it 'insert'), if the read is in the negative strand, this is the first base before the
      * beginning of the fragment.
-     *
+     * <p/>
      * There are two cases we need to treat here:
-     *
+     * <p/>
      * 1) Our read is in the reverse strand :
-     *
-     *     <----------------------| *
-     *   |--------------------->
-     *
-     *   in these cases, the adaptor boundary is at the mate start (minus one)
-     *
+     * <p/>
+     * <----------------------| *
+     * |--------------------->
+     * <p/>
+     * in these cases, the adaptor boundary is at the mate start (minus one)
+     * <p/>
      * 2) Our read is in the forward strand :
-     *
-     *   |---------------------->   *
-     *     <----------------------|
-     *
-     *   in these cases the adaptor boundary is at the start of the read plus the inferred insert size (plus one)
+     * <p/>
+     * |---------------------->   *
+     * <----------------------|
+     * <p/>
+     * in these cases the adaptor boundary is at the start of the read plus the inferred insert size (plus one)
      *
      * @param read the read being tested for the adaptor boundary
-     * @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. NULL if the read is unmapped or the insert size cannot be determined (and is necessary for the calculation).
+     * @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. NULL if the read is unmapped or the mate is mapped to another contig.
      */
     public static Integer getAdaptorBoundary(final SAMRecord read) {
-        if ( read.getReadUnmappedFlag() )
-            return null;                                             // don't worry about unmapped pairs
+        final int insertSize = Math.abs(read.getInferredInsertSize());    // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value)
 
-        final int isize = Math.abs(read.getInferredInsertSize());    // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value)
-        int adaptorBoundary;                                         // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read)
+        if (insertSize == 0 || read.getReadUnmappedFlag())                // no adaptors in reads with mates in another
+            return null;                                                  // chromosome or unmapped pairs
 
-        if ( read.getReadNegativeStrandFlag() )
-            adaptorBoundary = read.getMateAlignmentStart() - 1;      // case 1 (see header)
-        else if (isize > 0)
-            adaptorBoundary = read.getAlignmentStart() + isize + 1;  // case 2 (see header)
+        int adaptorBoundary;                                              // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read)
+        if (read.getReadNegativeStrandFlag())
+            adaptorBoundary = read.getMateAlignmentStart() - 1;           // case 1 (see header)
         else
-            return null;                                             // this is a case 2 where for some reason we cannot estimate the insert size
+            adaptorBoundary = read.getAlignmentStart() + insertSize + 1;  // case 2 (see header)
 
         return adaptorBoundary;
     }
@@ -262,14 +264,15 @@ public class ReadUtils {
 
     /**
      * If a read starts in INSERTION, returns the first element length.
-     *
+     * <p/>
      * Warning: If the read has Hard or Soft clips before the insertion this function will return 0.
+     *
      * @param read
      * @return the length of the first insertion, or 0 if there is none (see warning).
      */
     public final static int getFirstInsertionOffset(SAMRecord read) {
         CigarElement e = read.getCigar().getCigarElement(0);
-        if ( e.getOperator() == CigarOperator.I )
+        if (e.getOperator() == CigarOperator.I)
             return e.getLength();
         else
             return 0;
@@ -277,14 +280,15 @@ public class ReadUtils {
 
     /**
      * If a read ends in INSERTION, returns the last element length.
-     *
+     * <p/>
      * Warning: If the read has Hard or Soft clips after the insertion this function will return 0.
+     *
      * @param read
      * @return the length of the last insertion, or 0 if there is none (see warning).
      */
     public final static int getLastInsertionOffset(SAMRecord read) {
         CigarElement e = read.getCigar().getCigarElement(read.getCigarLength() - 1);
-        if ( e.getOperator() == CigarOperator.I )
+        if (e.getOperator() == CigarOperator.I)
             return e.getLength();
         else
             return 0;
@@ -293,7 +297,8 @@ public class ReadUtils {
     /**
      * Determines what is the position of the read in relation to the interval.
      * Note: This function uses the UNCLIPPED ENDS of the reads for the comparison.
-     * @param read the read
+     *
+     * @param read     the read
      * @param interval the interval
      * @return the overlap type as described by ReadAndIntervalOverlap enum (see above)
      */
@@ -304,30 +309,30 @@ public class ReadUtils {
         int uStart = read.getUnclippedStart();
         int uStop = read.getUnclippedEnd();
 
-        if ( !read.getReferenceName().equals(interval.getContig()) )
+        if (!read.getReferenceName().equals(interval.getContig()))
             return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG;
 
-        else if ( uStop < interval.getStart() )
+        else if (uStop < interval.getStart())
             return ReadAndIntervalOverlap.NO_OVERLAP_LEFT;
 
-        else if ( uStart > interval.getStop() )
+        else if (uStart > interval.getStop())
             return ReadAndIntervalOverlap.NO_OVERLAP_RIGHT;
 
-        else if ( sStop < interval.getStart() )
+        else if (sStop < interval.getStart())
             return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_LEFT;
 
-        else if ( sStart > interval.getStop() )
+        else if (sStart > interval.getStop())
             return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_RIGHT;
 
-        else if ( (sStart >= interval.getStart()) &&
-                  (sStop <= interval.getStop()) )
+        else if ((sStart >= interval.getStart()) &&
+                (sStop <= interval.getStop()))
             return ReadAndIntervalOverlap.OVERLAP_CONTAINED;
 
-        else if ( (sStart < interval.getStart()) &&
-                  (sStop > interval.getStop()) )
+        else if ((sStart < interval.getStart()) &&
+                (sStop > interval.getStop()))
             return ReadAndIntervalOverlap.OVERLAP_LEFT_AND_RIGHT;
 
-        else if ( (sStart < interval.getStart()) )
+        else if ((sStart < interval.getStart()))
             return ReadAndIntervalOverlap.OVERLAP_LEFT;
 
         else
@@ -359,12 +364,12 @@ public class ReadUtils {
 
     /**
      * Returns the read coordinate corresponding to the requested reference coordinate.
-     *
+     * <p/>
      * WARNING: if the requested reference coordinate happens to fall inside a deletion in the read, this function
      * will return the last read base before the deletion. This function returns a
      * Pair(int readCoord, boolean fallsInsideDeletion) so you can choose which readCoordinate to use when faced with
      * a deletion.
-     *
+     * <p/>
      * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int, ClippingTail) instead to get a
      * pre-processed result according to normal clipping needs. Or you can use this function and tailor the
      * behavior to your needs.
@@ -403,7 +408,7 @@ public class ReadUtils {
 
             if (goalReached) {
                 // Is this base's reference position within this cigar element? Or did we use it all?
-                boolean endsWithinCigar = shift <  cigarElement.getLength();
+                boolean endsWithinCigar = shift < cigarElement.getLength();
 
                 // If it isn't, we need to check the next one. There should *ALWAYS* be a next one
                 // since we checked if the goal coordinate is within the read length, so this is just a sanity check.
@@ -416,7 +421,7 @@ public class ReadUtils {
                 if (endsWithinCigar)
                     fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
 
-                // if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
+                    // if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
                 else {
                     nextCigarElement = cigarElementIterator.next();
 
@@ -437,21 +442,21 @@ public class ReadUtils {
                 if (!fallsInsideDeletion && cigarElement.getOperator().consumesReadBases())
                     readBases += shift;
 
-                // If we reached our goal inside a deletion, but the deletion is the next cigar element then we need
-                // to add the shift of the current cigar element but go back to it's last element to return the last
-                // base before the deletion (see warning in function contracts)
+                    // If we reached our goal inside a deletion, but the deletion is the next cigar element then we need
+                    // to add the shift of the current cigar element but go back to it's last element to return the last
+                    // base before the deletion (see warning in function contracts)
                 else if (fallsInsideDeletion && !endsWithinCigar)
                     readBases += shift - 1;
 
-                // If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
+                    // If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
                 else if (fallsInsideDeletion && endsWithinCigar)
                     readBases--;
-                }
             }
+        }
+
+        if (!goalReached)
+            throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
 
-            if (!goalReached)
-                throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
-        
 
         return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
     }
@@ -460,7 +465,7 @@ public class ReadUtils {
      * Compares two SAMRecords only the basis on alignment start.  Note that
      * comparisons are performed ONLY on the basis of alignment start; any
      * two SAM records with the same alignment start will be considered equal.
-     *
+     * <p/>
      * Unmapped alignments will all be considered equal.
      */
 
@@ -474,7 +479,7 @@ public class ReadUtils {
     /**
      * Is a base inside a read?
      *
-     * @param read the read to evaluate
+     * @param read                the read to evaluate
      * @param referenceCoordinate the reference coordinate of the base to test
      * @return true if it is inside the read, false otherwise.
      */
@@ -497,6 +502,4 @@ public class ReadUtils {
     }
 
 
-
-
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
index 8bea5385a..e26d6174b 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
@@ -29,12 +29,10 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
         String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
                  + "-R " + hg18Reference
                 + " -show_indels -o %s";
-        String expected_md5="da2a02d02abac9de14cc4b187d8595a1";
+        String expected_md5="06eedc2e7927650961d99d703f4301a4";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
         executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
 
-        // before Adaptor clipping
-        //        String expected_md5="06eedc2e7927650961d99d703f4301a4";
 
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index fa0b62cfd..8b101d1d5 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ac5f409856a1b79316469733e62abb91"));
+                Arrays.asList("e70eb5f80c93e366dcbe3cf684c154e4"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("f9aa7bee5a61ac1a9187d0cf1e8af471"));
+                Arrays.asList("2977bb30c8b84a5f4094fe6090658561"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("6f27fd863b6718d59d2a2d8e2a20bcae"));
+                Arrays.asList("1e52761fdff73a5361b5eb0a6e5d9dad"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("40bbd3d5a2397a007c0e74211fb33433"));
+                Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("40622d39072b298440a77ecc794116e7"));
+                Arrays.asList("bb4eebfaffc230cb8a31e62e7b53a300"));
         executeTest("test exclude annotations", spec);
     }
 
@@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("31faae1bc588d195ff553cf6c47fabfa"));
+                Arrays.asList("062155edec46a8c52243475fbf3a2943"));
         executeTest("test overwriting header", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
index 186e5c3b7..02332b64e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
@@ -32,13 +32,13 @@ import java.util.Arrays;
 public class CallableLociWalkerIntegrationTest extends WalkerTest {
     final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
 
-    final static String SUMMARY_MD5 = "cd597a8dae35c226a2cb110b1c9f32d5";
+    final static String SUMMARY_MD5 = "ffdbd9cdcb4169ebed5ae4bec797260f";
 
     @Test
     public void testCallableLociWalkerBed() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("c86ac1ef404c11d5e5452e020c8f7ce9", SUMMARY_MD5));
+                Arrays.asList("9e4ec9c23f21a8162d27a39ab057398c", SUMMARY_MD5));
         executeTest("formatBed", spec);
     }
 
@@ -46,7 +46,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalkerPerBase() {
         String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("d8536a55fe5f6fdb1ee6c9511082fdfd", SUMMARY_MD5));
+                Arrays.asList("e6044b4495ef24f542403e6a94437068", SUMMARY_MD5));
         executeTest("format_state_per_base", spec);
     }
     
@@ -62,7 +62,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalker3() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("bc966060184bf4605a31da7fe383464e", "d624eda8f6ed14b9251ebeec73e37867"));
+                Arrays.asList("4496551d4493857e5153d8172965e527", "b0667e31af9aec02eaf73ca73ec16937"));
         executeTest("formatBed lots of arguments", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
index f4cd4968b..84603f066 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
@@ -61,13 +61,13 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
         File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
 
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("5b6c16a1c667c844882e9dce71454fc4",baseOutputFile);
-        spec.addAuxFile("fc161ec1b61dc67bc6a5ce36cb2d02c9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
-        spec.addAuxFile("89321bbfb76a4e1edc0905d50503ba1f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
+        spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
+        spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
+        spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
         spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
-        spec.addAuxFile("4dd16b659065e331ed4bd3ab0dae6c1b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
-        spec.addAuxFile("2be0c18b501f4a3d8c5e5f99738b4713", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
-        spec.addAuxFile("5a26ef61f586f58310812580ce842462", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+        spec.addAuxFile("cb73a0fa0cee50f1fb8f249315d38128", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
+        spec.addAuxFile("4ec920335d4b9573f695c39d62748089", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
 
 
         execute("testMapQ0Only",spec);
@@ -84,7 +84,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
         File baseOutputFile = this.createTempFile("testManySamples",".tmp");
         
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("d73fa1fc492f7dcc1d75056f8c12c92a",baseOutputFile);
+        spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
 
         execute("testLotsOfSamples",spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
index 9d6638d53..f2f72978f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -55,25 +55,25 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         spec.setOutputFileLocation(baseOutputFile);
 
         // now add the expected files that get generated
-        spec.addAuxFile("19e862f7ed3de97f2569803f766b7433", baseOutputFile);
-        spec.addAuxFile("c64cc5636d4880b80b71169ed1832cd7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
-        spec.addAuxFile("1a8ba07a60e55f9fdadc89d00b1f3394", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
-        spec.addAuxFile("0075cead73a901e3a9d07c5d9c2b75f4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
-        spec.addAuxFile("d757be2f953f893e66eff1ef1f0fff4e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
-        spec.addAuxFile("de08996729c774590d6a4954c906fe84", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
-        spec.addAuxFile("58ad39b100d1f2af7d119f28ba626bfd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
-        spec.addAuxFile("0b4ce6059e6587ae5a986afbbcc7d783", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
-        spec.addAuxFile("adc2b2babcdd72a843878acf2d510ca7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
-        spec.addAuxFile("884281c139241c5db3c9f90e8684d084", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
-        spec.addAuxFile("b90636cad74ff4f6b9ff9a596e145bd6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
-        spec.addAuxFile("ad540b355ef90c566bebaeabd70026d2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
-        spec.addAuxFile("27fe09a02a5b381e0ed633587c0f4b23", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
-        spec.addAuxFile("5fcd53b4bd167b5e6d5f92329cf8678e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
-        spec.addAuxFile("7a2a19e54f73a8e07de2f020f1f913dd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
-        spec.addAuxFile("852a079c5e9e93e7daad31fd6a9f4a49", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
-        spec.addAuxFile("0828762842103edfaf115ef4e50809c6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
-        spec.addAuxFile("5c5aeb28419bba1decb17f8a166777f2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
-        spec.addAuxFile("e5fd6216b3d6a751f3a90677b4e5bf3c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+        spec.addAuxFile("2f072fd8b41b5ac1108797f89376c797", baseOutputFile);
+        spec.addAuxFile("d17ac7cc0b58ba801d2b0727a363d615", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
+        spec.addAuxFile("c05190c9e6239cdb1cd486edcbc23505", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
+        spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
+        spec.addAuxFile("c94a52b4e73a7995319e0b570c80d2f7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
+        spec.addAuxFile("1970a44efb7ace4e51a37f0bd2dc84d1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
+        spec.addAuxFile("c321c542be25359d2e26d45cbeb6d7ab", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
+        spec.addAuxFile("9023cc8939777d515cd2895919a99688", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
+        spec.addAuxFile("3597b69e90742c5dd7c83fbc74d079f3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
+        spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
+        spec.addAuxFile("1a6ea3aa759fb154ccc4e171ebca9d02", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
+        spec.addAuxFile("b492644ff06b4ffb044d5075cd168abf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
+        spec.addAuxFile("77cef87dc4083a7b60b7a7b38b4c0bd8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
+        spec.addAuxFile("8e1adbe37b98bb2271ba13932d5c947f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
+        spec.addAuxFile("761d2f9daf2ebaf43abf65c8fd2fcd05", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
+        spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
+        spec.addAuxFile("0582b4681dbc02ece2dfe2752dcfd228", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("0685214965bf1863f7ce8de2e38af060", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
+        spec.addAuxFile("7a0cd8a5ebaaa82621fd3b5aed9c32fe", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
 
         execute("testBaseOutputNoFiltering",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 d4518078b..26d0d4ee3 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
@@ -227,7 +227,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("d87ce4b405d4f7926d1c36aee7053975"));
+                Arrays.asList("b11df6587e4e16cb819d76a900446946"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -255,7 +255,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("c5989e5d67d9e5fe8c5c956f12a975da"));
+                 Arrays.asList("59068bc8888ad5f08790946066d76602"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -265,7 +265,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("daca0741278de32e507ad367e67753b6"));
+                Arrays.asList("fa4f3ee67d98b64102a8a3ec81a3bc81"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
     }
 
@@ -275,7 +275,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("0ccc4e876809566510429c64adece2c7"));
+                Arrays.asList("df90890e43d735573a3b3e4f289ca46b"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index b4b1f7b8e..d45e663b0 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -5,11 +5,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Arrays;
-import java.util.List;
 import java.io.File;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     static HashMap<String, String> paramsFiles = new HashMap<String, String>();
@@ -32,10 +32,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @DataProvider(name = "cctestdata")
     public Object[][] createCCTestData() {
 
-        new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9469d6b65880abe4e5babc1c1a69889d" );
+        new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "ab4940a16ab990181bd8368c76b23853" );
         new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941");
         new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "36c0c467b6245c2c6c4e9c956443a154" );
-        new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "ed15f8bf03bb2ea9b7c26844be829c0d" );
+        new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "955a8fa2ddb2b04c406766ccd9ac45cc" );
         return CCTest.getTests(CCTest.class);
     }
 
@@ -89,10 +89,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
     @DataProvider(name = "trtestdata")
     public Object[][] createTRTestData() {
-        new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" );
+        new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
         new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5");
         new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b2f4757bc47cf23bd9a09f756c250787" );
-        new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "313a21a8a88e3460b6e71ec5ffc50f0f" );
+        new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "502c7df4d4923c4d078b014bf78bed34" );
 
         return TRTest.getTests(TRTest.class);
     }
@@ -123,7 +123,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesUseOriginalQuals() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "bd8288b1fc7629e2e8c2cf7f65fefa8f");
+        e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "0b88d0e8c97e83bdeee2064b6730abff");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -147,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" );
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -176,7 +176,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1f643bca090478ba68aac88db835a629" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "8379f24cf5312587a1f92c162ecc220f" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -230,7 +230,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesBED() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b00e99219aeafe2516c6232b7d6a0a00");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7e973328751d233653530245d404a64d");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -254,7 +254,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCFPlusDBsnp() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b92788ce92f49415af3a75a2e4a2b33");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "fd9e37879069aa6d84436c25e472b9e9");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -282,7 +282,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "f34f7141351a5dbf9664c67260f94e96" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "828d247c6e8ef5ebdf3603dc0ce79f61" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
index e9269ff48..b9f831028 100755
--- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
@@ -1,12 +1,8 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
@@ -16,12 +12,12 @@ public class ReadUtilsUnitTest extends BaseTest {
     GATKSAMRecord read, reducedRead;
     final static String BASES = "ACTG";
     final static String QUALS = "!+5?";
-    final private static byte[] REDUCED_READ_COUNTS =     new byte[]{10, 20, 30, 40, 1};
+    final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
     final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9};  // just the offsets
 
     @BeforeTest
     public void init() {
-        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
         read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
         read.setReadUnmappedFlag(true);
         read.setReadBases(new String(BASES).getBytes());
@@ -39,15 +35,15 @@ public class ReadUtilsUnitTest extends BaseTest {
         Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
 
         Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
-        for ( int i = 0; i < reducedRead.getReadLength(); i++) {
+        for (int i = 0; i < reducedRead.getReadLength(); i++) {
             Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
         }
     }
 
     @Test
     public void testReducedReadPileupElement() {
-        PileupElement readp = new PileupElement(read,0);
-        PileupElement reducedreadp = new PileupElement(reducedRead,0);
+        PileupElement readp = new PileupElement(read, 0);
+        PileupElement reducedreadp = new PileupElement(reducedRead, 0);
 
         Assert.assertFalse(readp.isReducedRead());
 
@@ -58,14 +54,14 @@ public class ReadUtilsUnitTest extends BaseTest {
 
     @Test
     public void testGetAdaptorBoundary() {
-        final byte [] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};
-        final byte [] quals = {30, 30, 30, 30, 30, 30, 30, 30};
+        final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};
+        final byte[] quals = {30, 30, 30, 30, 30, 30, 30, 30};
         final String cigar = "8M";
         final int fragmentSize = 10;
         final int mateStart = 1000;
         final int BEFORE = mateStart - 2;
         final int AFTER = mateStart + 2;
-        int myStart, boundary;
+        Integer myStart, boundary;
 
         GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar);
         read.setMateAlignmentStart(mateStart);
@@ -76,28 +72,41 @@ public class ReadUtilsUnitTest extends BaseTest {
         read.setAlignmentStart(myStart);
         read.setReadNegativeStrandFlag(false);
         boundary = ReadUtils.getAdaptorBoundary(read);
-        Assert.assertEquals(boundary, myStart + fragmentSize + 1);
+        Assert.assertEquals(boundary.intValue(), myStart + fragmentSize + 1);
 
         // Test case 2: positive strand, second read
         myStart = AFTER;
         read.setAlignmentStart(myStart);
         read.setReadNegativeStrandFlag(false);
         boundary = ReadUtils.getAdaptorBoundary(read);
-        Assert.assertEquals(boundary, myStart + fragmentSize + 1);
+        Assert.assertEquals(boundary.intValue(), myStart + fragmentSize + 1);
 
         // Test case 3: negative strand, second read
         myStart = AFTER;
         read.setAlignmentStart(myStart);
         read.setReadNegativeStrandFlag(true);
         boundary = ReadUtils.getAdaptorBoundary(read);
-        Assert.assertEquals(boundary, mateStart - 1);
+        Assert.assertEquals(boundary.intValue(), mateStart - 1);
 
         // Test case 4: negative strand, first read
         myStart = BEFORE;
         read.setAlignmentStart(myStart);
         read.setReadNegativeStrandFlag(true);
         boundary = ReadUtils.getAdaptorBoundary(read);
-        Assert.assertEquals(boundary, mateStart - 1);
+        Assert.assertEquals(boundary.intValue(), mateStart - 1);
 
+        // Test case 5: mate is mapped to another chromosome (test both strands)
+        read.setInferredInsertSize(0);
+        read.setReadNegativeStrandFlag(true);
+        boundary = ReadUtils.getAdaptorBoundary(read);
+        Assert.assertNull(boundary);
+        read.setReadNegativeStrandFlag(false);
+        boundary = ReadUtils.getAdaptorBoundary(read);
+        Assert.assertNull(boundary);
+
+        // Test case 6: read is unmapped
+        read.setReadUnmappedFlag(true);
+        boundary = ReadUtils.getAdaptorBoundary(read);
+        Assert.assertNull(boundary);
     }
 }
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2125.jar b/settings/repository/edu.mit.broad/picard-private-parts-2125.jar
deleted file mode 100644
index 70c589572..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-2125.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2164.jar b/settings/repository/edu.mit.broad/picard-private-parts-2164.jar
new file mode 100644
index 000000000..4465f91f5
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-2164.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2125.xml b/settings/repository/edu.mit.broad/picard-private-parts-2164.xml
similarity index 58%
rename from settings/repository/edu.mit.broad/picard-private-parts-2125.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-2164.xml
index 0758c94cd..6a22ea2c3 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-2125.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-2164.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2125" status="integration" publication="20111024162900" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2164" status="integration" publication="20111229115300" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.57.1030.xml b/settings/repository/net.sf/picard-1.57.1030.xml
deleted file mode 100644
index 50e2db846..000000000
--- a/settings/repository/net.sf/picard-1.57.1030.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.57.1030" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.57.1030.jar b/settings/repository/net.sf/picard-1.58.1057.jar
similarity index 88%
rename from settings/repository/net.sf/picard-1.57.1030.jar
rename to settings/repository/net.sf/picard-1.58.1057.jar
index 0ce2cb0dc..4a82a3058 100644
Binary files a/settings/repository/net.sf/picard-1.57.1030.jar and b/settings/repository/net.sf/picard-1.58.1057.jar differ
diff --git a/settings/repository/net.sf/picard-1.58.1057.xml b/settings/repository/net.sf/picard-1.58.1057.xml
new file mode 100644
index 000000000..15c5b5620
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.58.1057.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.58.1057" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.57.1030.xml b/settings/repository/net.sf/sam-1.57.1030.xml
deleted file mode 100644
index a5dfe0718..000000000
--- a/settings/repository/net.sf/sam-1.57.1030.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.57.1030" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.57.1030.jar b/settings/repository/net.sf/sam-1.58.1057.jar
similarity index 91%
rename from settings/repository/net.sf/sam-1.57.1030.jar
rename to settings/repository/net.sf/sam-1.58.1057.jar
index 2404c9986..804e21b61 100644
Binary files a/settings/repository/net.sf/sam-1.57.1030.jar and b/settings/repository/net.sf/sam-1.58.1057.jar differ
diff --git a/settings/repository/net.sf/sam-1.58.1057.xml b/settings/repository/net.sf/sam-1.58.1057.xml
new file mode 100644
index 000000000..4f0dfe44e
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.58.1057.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.58.1057" status="release" />
+</ivy-module>