diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index fed2c995e..c6e28df05 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
+import com.google.java.contract.Ensures;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Input;
@@ -75,6 +76,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     }
 
     // Determine probability of active status over the AlignmentContext
+    @Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
     public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
 
     // Map over the ActiveRegion
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index 579b84d96..0da23077d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -283,7 +283,7 @@ public class DiffEngine {
         GATKReport report = new GATKReport();
         final String tableName = "differences";
         // TODO for Geraldine -- link needs to be updated below
-        report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3);
+        report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
         final GATKReportTable table = report.getTable(tableName);
         table.addColumn("Difference");
         table.addColumn("NumberOfOccurrences");
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index d8ae6b28b..eda43e6a5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 
 @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
-    private static final boolean DEBUG = false;
+    @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
+    protected boolean DEBUG = false;
     /**
      * The VCF file we are phasing variants from.
      *
@@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         }
 
         if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n");
-        MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, true);
+        MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, DEBUG);
         double posteriorProb = maxHapQual.maxEntry.getScore().getValue();
 
         if (DEBUG)
@@ -971,7 +972,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) {
             // Marginalize each haplotype to its first 2 positions:
             hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable);
-            if (DEBUG && printDebug)
+            if (printDebug)
                 logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n");
 
             calculateMaxHapAndPhasingQuality(hapTable, printDebug);
@@ -981,7 +982,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
         private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
             hapTable.normalizeScores();
-            if (DEBUG && printDebug)
+            if (printDebug)
                 logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n");
 
             // Determine the phase at this position:
diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
index e4c7b2db0..66504da11 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.traversals;
 
+import com.google.java.contract.PreconditionError;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
@@ -52,6 +53,10 @@ public class TraverseActiveRegionsTest extends BaseTest {
             this.prob = 1.0;
         }
 
+        public DummyActiveRegionWalker(double constProb) {
+            this.prob = constProb;
+        }
+
         @Override
         public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
             isActiveCalls.add(ref.getLocus());
@@ -96,8 +101,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
         intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
         intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
         intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
-        // TODO: this fails!
-        //intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 20000));
+        intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
         intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
 
         reads = new ArrayList<SAMRecord>();
@@ -105,12 +109,11 @@ public class TraverseActiveRegionsTest extends BaseTest {
         reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
         reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
         reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009));
-        reads.add(buildSAMRecord("boundary_unequal", "1", 1995, 2050));
+        reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
         reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
         reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
         reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
-        // TODO
-        //reads.add(buildSAMRecord("simple20", "20", 10100, 10150));
+        reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
     }
 
     @Test
@@ -134,6 +137,18 @@ public class TraverseActiveRegionsTest extends BaseTest {
         return activeIntervals;
     }
 
+    @Test (expectedExceptions = PreconditionError.class)
+    public void testIsActiveRangeLow () {
+        DummyActiveRegionWalker walker = new DummyActiveRegionWalker(-0.1);
+        getActiveRegions(walker, intervals).values();
+    }
+
+    @Test (expectedExceptions = PreconditionError.class)
+    public void testIsActiveRangeHigh () {
+        DummyActiveRegionWalker walker = new DummyActiveRegionWalker(1.1);
+        getActiveRegions(walker, intervals).values();
+    }
+
     @Test
     public void testActiveRegionCoverage() {
         DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
@@ -199,14 +214,12 @@ public class TraverseActiveRegionsTest extends BaseTest {
         // simple: Primary in 1:1-999
         // overlap_equal: Primary in 1:1-999
         // overlap_unequal: Primary in 1:1-999
-        // boundary_equal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
-        // boundary_unequal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
+        // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
+        // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
         // extended_only: Extended in 1:2000-2999
         // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
         // outside_intervals: none
-
-        // TODO
-        // simple20: Primary in 20:10000-20000
+        // simple20: Primary in 20:10000-10100
 
         Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
         ActiveRegion region;
@@ -221,28 +234,43 @@ public class TraverseActiveRegionsTest extends BaseTest {
         verifyReadNotPlaced(region, "extended_only");
         // TODO: fail verifyReadNonPrimary(region, "extended_and_np");
         verifyReadNotPlaced(region, "outside_intervals");
+        verifyReadNotPlaced(region, "simple20");
 
         region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
 
         verifyReadNotPlaced(region, "simple");
         verifyReadNotPlaced(region, "overlap_equal");
         verifyReadNotPlaced(region, "overlap_unequal");
-        // TODO: fail verifyReadPrimary(region, "boundary_equal");
-        // TODO: fail verifyReadNonPrimary(region, "boundary_unequal");
+        // TODO: fail verifyReadNonPrimary(region, "boundary_equal");
+        verifyReadPrimary(region, "boundary_unequal");
         verifyReadNotPlaced(region, "extended_only");
         // TODO: fail verifyReadPrimary(region, "extended_and_np");
         verifyReadNotPlaced(region, "outside_intervals");
+        verifyReadNotPlaced(region, "simple20");
 
         region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
 
         verifyReadNotPlaced(region, "simple");
         verifyReadNotPlaced(region, "overlap_equal");
         verifyReadNotPlaced(region, "overlap_unequal");
-        // TODO: fail verifyReadNonPrimary(region, "boundary_equal");
-        verifyReadPrimary(region, "boundary_unequal");
+        verifyReadPrimary(region, "boundary_equal");
+        // TODO: fail verifyReadNonPrimary(region, "boundary_unequal");
         // TODO: fail verifyReadExtended(region, "extended_only");
         // TODO: fail verifyReadExtended(region, "extended_and_np");
         verifyReadNotPlaced(region, "outside_intervals");
+        verifyReadNotPlaced(region, "simple20");
+
+        region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
+
+        verifyReadNotPlaced(region, "simple");
+        verifyReadNotPlaced(region, "overlap_equal");
+        verifyReadNotPlaced(region, "overlap_unequal");
+        verifyReadNotPlaced(region, "boundary_equal");
+        verifyReadNotPlaced(region, "boundary_unequal");
+        verifyReadNotPlaced(region, "extended_only");
+        verifyReadNotPlaced(region, "extended_and_np");
+        verifyReadNotPlaced(region, "outside_intervals");
+        verifyReadPrimary(region, "simple20");
 
         // TODO: more tests and edge cases
     }
@@ -282,6 +310,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
         for (LocusShardDataProvider dataProvider : createDataProviders(intervals))
             t.traverse(walker, dataProvider, 0);
 
+        t.endTraversal(walker, 0);
+
         return walker.mappedActiveRegions;
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
index f3daa9e4c..3ad438b26 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
@@ -793,7 +793,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
         int sampleI = 0;
         for ( final List<Allele> alleles : Utils.makePermutations(vc.getAlleles(), 2, true) ) {
-            genotypes.add(GenotypeBuilder.create("sample" + sampleI, alleles));
+            genotypes.add(GenotypeBuilder.create("sample" + sampleI++, alleles));
         }
         genotypes.add(GenotypeBuilder.createMissing("missing", 2));