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 96f327631..992a411ea 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -55,6 +55,7 @@ import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -129,6 +130,7 @@ import java.util.*;
 @PartitionBy(PartitionType.LOCUS)
 @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
 @ActiveRegionExtension(extension=65, maxRegion=300)
+//@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=5)
 public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
 
     /**
@@ -175,6 +177,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     @Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "If specified, use the contamination-filtered read maps for the purposes of annotating variants", required=false)
     protected boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
 
+    @Hidden
+    @Argument(fullName="justDetermineActiveRegions", shortName="justDetermineActiveRegions", doc = "If specified, the HC won't actually do any assembly or calling, it'll just run the upfront active region determination code.  Useful for benchmarking and scalability testing", required=false)
+    protected boolean justDetermineActiveRegions = false;
+
     /**
      * rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate.
      * dbSNP is not used in any way for the calculations themselves.
@@ -403,6 +409,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
 
     @Override
     public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
+        if ( justDetermineActiveRegions )
+            // we're benchmarking ART and/or the active region determination code in the HC, just leave without doing any work
+            return 1;
 
         final ArrayList<VariantContext> activeAllelesToGenotype = new ArrayList<VariantContext>();
 
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 142fa39bf..060fda75a 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
@@ -115,6 +115,11 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
     }
 
+    // That problem bam came from a user on the forum and it spotted a problem where the ReadClipper
+    // was modifying the GATKSamRecord and that was screwing up the traversal engine from map call to
+    // map call. So the test is there for consistency but not for correctness. I'm not sure we can trust
+    // any of the calls in that region because it is so messy. The only thing I would maybe be worried about is
+    // that the three calls that are missing happen to all be the left most calls in the region
     @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 -L 4:49139026-49139965";