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 0d6e29fe9..ee9993b4f 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
@@ -794,7 +794,7 @@ public class GenotypingEngine {
         return vcs;
     }
 
-    private static class Event {
+    protected static class Event {
         public VariantContext vc;
 
         public Event( final VariantContext vc ) {
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 c416938cd..292bea50d 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
@@ -46,11 +46,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broad.tribble.TribbleIndexedFeatureReader;
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFCodec;
 import org.testng.annotations.Test;
 
-import java.util.Arrays;
-import java.util.Collections;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.*;
 
 public class HaplotypeCallerIntegrationTest extends WalkerTest {
     final static String REF = b37KGReference;
@@ -88,6 +99,11 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                 "70bd5d0805bf6f51e5f61b377526c979");
     }
 
+    @Test
+    public void testHaplotypeCallerInsertionOnEdgeOfContig() {
+        HCTest(CEUTRIO_MT_TEST_BAM, "-dcov 90 -L MT:1-10", "7f1fb8f9587f64643f6612ef1dd6d4ae");
+    }
+
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
@@ -99,9 +115,41 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "4141b4c24a136a3fe4c0b0a4c231cdfa");
     }
 
+    private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
+        try {
+            final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(new File(b37KGReference));
+            final GenomeLocParser parser = new GenomeLocParser(fasta.getSequenceDictionary());
+
+            final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
+            final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
+            for( final File vcf : executeTest("testHaplotypeCallerNearbySmallIntervals: args=" + args, spec).getFirst() ) {
+                if( containsDuplicateRecord(vcf, parser) ) {
+                    throw new IllegalStateException("Duplicate records detected but there should be none.");
+                }
+            }
+        } catch( FileNotFoundException e ) {
+            throw new IllegalStateException("Could not find the b37 reference file.");
+        }
+    }
+
+    private boolean containsDuplicateRecord( final File vcf, final GenomeLocParser parser ) {
+        final List<Pair<GenomeLoc, GenotypingEngine.Event>> VCs = new ArrayList<Pair<GenomeLoc, GenotypingEngine.Event>>();
+        try {
+            for( final VariantContext vc :  GATKVCFUtils.readVCF(vcf).getSecond() ) {
+                VCs.add(new Pair<GenomeLoc, GenotypingEngine.Event>(parser.createGenomeLoc(vc), new GenotypingEngine.Event(vc)));
+            }
+        } catch( IOException e ) {
+            throw new IllegalStateException("Somehow the temporary VCF from the integration test could not be read.");
+        }
+
+        final Set<Pair<GenomeLoc, GenotypingEngine.Event>> VCsAsSet = new HashSet<Pair<GenomeLoc, GenotypingEngine.Event>>(VCs);
+        return VCsAsSet.size() != VCs.size(); // The set will remove duplicate Events.
+    }
+
+
     @Test
-    public void testHaplotypeCallerInsertionOnEdgeOfContig() {
-        HCTest(CEUTRIO_MT_TEST_BAM, "-dcov 90 -L MT:1-10", "7f1fb8f9587f64643f6612ef1dd6d4ae");
+    public void testHaplotypeCallerNearbySmallIntervals() {
+        HCTestNearbySmallIntervals(NA12878_BAM, "", "b9d614efdaf38b87b459df421aab93a7");
     }
 
     // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index 64c6d5094..7b831db32 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -70,7 +70,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
     protected final static Logger logger = Logger.getLogger(TraversalEngine.class);
     protected final static boolean LOG_READ_CARRYING = false;
 
-    // set by the tranversal
+    // set by the traversal
     private boolean walkerHasPresetRegions = false;
     private int activeRegionExtension = -1;
     private int maxRegionSize = -1;
@@ -112,7 +112,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
         activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), engine.getIntervals(), BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma);
 
         if ( walkerHasPresetRegions ) {
-            // we load all of the preset locations into the
+            // we load all of the preset locations into the workQueue
             for ( final GenomeLoc loc : this.walker.getPresetActiveRegions()) {
                 workQueue.add(new ActiveRegion(loc, null, true, engine.getGenomeLocParser(), getActiveRegionExtension()));
             }
@@ -190,6 +190,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
      * @param read the read we want to test if it's already been seen in the last shard
      * @return true if read would have appeared in the last shard, false otherwise
      */
+    @Requires({"read != null"})
     private boolean appearedInLastShard(final GenomeLoc locOfLastReadAtTraversalStart, final GATKSAMRecord read) {
         if ( locOfLastReadAtTraversalStart == null )
             // we're in the first shard, so obviously the answer is no
@@ -285,6 +286,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
      *
      * @param read the last read we've seen during the traversal
      */
+    @Requires({"read != null"})
     protected void rememberLastReadLocation(final GATKSAMRecord read) {
         final GenomeLoc currentLocation = engine.getGenomeLocParser().createGenomeLoc(read);
         if ( spanOfLastReadSeen == null )
diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
index 39509e9df..ed541b070 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
@@ -41,7 +41,7 @@ import java.util.*;
  * @since Date created
  */
 public class ActivityProfile {
-    private final static int MAX_PROB_PROPOGATION_DISTANCE = 50;
+    private final static int MAX_PROB_PROPAGATION_DISTANCE = 50;
     protected final static double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author
 
     protected final List<ActivityProfileState> stateList;
@@ -98,7 +98,7 @@ public class ActivityProfile {
      */
     @Ensures("result >= 0")
     public int getMaxProbPropagationDistance() {
-        return MAX_PROB_PROPOGATION_DISTANCE;
+        return MAX_PROB_PROPAGATION_DISTANCE;
     }
 
     /**
@@ -210,7 +210,7 @@ public class ActivityProfile {
             contigLength = parser.getContigInfo(regionStartLoc.getContig()).getSequenceLength();
         } else {
             if ( regionStopLoc.getStart() != loc.getStart() - 1 )
-                throw new IllegalArgumentException("Bad add call to ActivityProfile: loc " + loc + " not immediate after last loc " + regionStopLoc );
+                throw new IllegalArgumentException("Bad add call to ActivityProfile: loc " + loc + " not immediately after last loc " + regionStopLoc );
             regionStopLoc = loc;
         }
 
@@ -239,7 +239,7 @@ public class ActivityProfile {
             throw new IllegalArgumentException("Must add state contiguous to existing states: adding " + stateToAdd);
 
         if ( position >= 0 ) {
-            // ignore states starting before this regions start
+            // ignore states starting before this region's start
             if ( position < size() ) {
                 stateList.get(position).isActiveProb += stateToAdd.isActiveProb;
             } else {
@@ -352,6 +352,12 @@ public class ActivityProfile {
         if ( stateList.isEmpty() )
             return null;
 
+        // If we are flushing the activity profile we need to trim off the excess states so that we don't create regions outside of our current processing interval
+        if( forceConversion ) {
+            final List<ActivityProfileState> statesToTrimAway = new ArrayList<ActivityProfileState>(stateList.subList(getSpan().size(), stateList.size()));
+            stateList.removeAll(statesToTrimAway);
+        }
+
         final ActivityProfileState first = stateList.get(0);
         final boolean isActiveRegion = first.isActiveProb > ACTIVE_PROB_THRESHOLD;
         final int offsetOfNextRegionEnd = findEndOfRegion(isActiveRegion, minRegionSize, maxRegionSize, forceConversion);