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 7bf518fd5..941dc66b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -257,7 +257,7 @@ public class VariantContextAdaptors {
                     else genotypeAlleles.add(refAllele);
                 }
 
-                Map<String, String> attributes = new HashMap<String, String>();
+                Map<String, Object> attributes = new HashMap<String, Object>();
                 Collection<Genotype> genotypes = new ArrayList<Genotype>();
                 MutableGenotype call = new MutableGenotype(name, genotypeAlleles);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 414ffa09c..a97117acd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -1061,7 +1061,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
 
         for ( String sample : normalSamples ) {
 
-            Map<String,?> attrs = call.makeStatsAttributes(null);
+            Map<String,Object> attrs = call.makeStatsAttributes(null);
 
             if ( call.isCall() ) // we made a call - put actual het genotype here:
                 genotypes.put(sample,new Genotype(sample,alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrs,false));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 4e4a1550d..4556692bd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -186,7 +186,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
      * File containing tribble-readable features for the IntervalStratificiation
      */
     @Input(fullName="stratIntervals", shortName="stratIntervals", doc="File containing tribble-readable features for the IntervalStratificiation", required=false)
-    protected IntervalBinding<Feature> intervalsFile = null;
+    public IntervalBinding<Feature> intervalsFile = null;
 
     // Variables
     private Set<SortableJexlVCMatchExp> jexlExpressions = new TreeSet<SortableJexlVCMatchExp>();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
index 3ab618496..8cc321ef5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
@@ -51,21 +51,21 @@ public class G1KPhaseITable extends VariantEvaluator {
     @DataPoint(description = "Number of SNPs")
     public long nSNPs = 0;
     @DataPoint(description = "SNP Novelty Rate")
-    public double SNPNoveltyRate = 0;
+    public String SNPNoveltyRate = "NA";
     @DataPoint(description = "Mean number of SNPs per individual")
     public long nSNPsPerSample = 0;
 
     @DataPoint(description = "Number of Indels")
     public long nIndels = 0;
     @DataPoint(description = "Indel Novelty Rate")
-    public double IndelNoveltyRate = 0;
+    public String IndelNoveltyRate = "NA";
     @DataPoint(description = "Mean number of Indels per individual")
     public long nIndelsPerSample = 0;
 
     @DataPoint(description = "Number of SVs")
     public long nSVs = 0;
     @DataPoint(description = "SV Novelty Rate")
-    public double SVNoveltyRate = 0;
+    public String SVNoveltyRate = "NA";
     @DataPoint(description = "Mean number of SVs per individual")
     public long nSVsPerSample = 0;
 
@@ -106,9 +106,6 @@ public class G1KPhaseITable extends VariantEvaluator {
         if ( eval == null || eval.isMonomorphic() ) return null;
 
         switch (eval.getType()) {
-//            case NO_VARIATION:
-//                // shouldn't get here
-//                break;
             case SNP:
             case INDEL:
             case SYMBOLIC:
@@ -139,11 +136,12 @@ public class G1KPhaseITable extends VariantEvaluator {
         return (int)(Math.round(sum / (1.0 * countsPerSample.size())));
     }
 
-    private final double noveltyRate(VariantContext.Type type) {
+    private final String noveltyRate(VariantContext.Type type) {
         int all = allVariantCounts.get(type);
         int known = knownVariantCounts.get(type);
         int novel = all - known;
-        return (novel / (1.0 * all));
+        double rate = (novel / (1.0 * all));
+        return all == 0 ? "NA" : String.format("%.2f", rate);
     }
 
     public void finalizeEvaluation() {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
index bf001588a..00a656cc6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
@@ -63,8 +63,8 @@ public class IntervalStratification extends VariantStratifier {
         if ( locs.isEmpty() )
             throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals.  Perhaps the file is malformed or empty?");
 
-        logger.info(String.format("Creating IntervalStratification containing %d intervals covering %d bp",
-                locs.size(), IntervalUtils.intervalSize(locs)));
+        logger.info(String.format("Creating IntervalStratification %s containing %d intervals covering %d bp",
+                getVariantEvalWalker().intervalsFile.getSource(), locs.size(), IntervalUtils.intervalSize(locs)));
 
         // set up the map from contig -> interval tree
         for ( final String contig : getVariantEvalWalker().getContigNames() )
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index e5b1a2de5..bed66a439 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -141,7 +141,7 @@ public class VCF3Codec extends AbstractVCFCodec {
 
             double GTQual = VariantContext.NO_NEG_LOG_10PERROR;
             Set<String> genotypeFilters = null;
-            Map<String, String> gtAttributes = null;
+            Map<String, Object> gtAttributes = null;
             String sampleName = sampleNameIterator.next();
 
             // check to see if the value list is longer than the key list, which is a problem
@@ -150,7 +150,7 @@ public class VCF3Codec extends AbstractVCFCodec {
 
             int genotypeAlleleLocation = -1;
             if (nGTKeys >= 1) {
-                gtAttributes = new HashMap<String, String>(nGTKeys - 1);
+                gtAttributes = new HashMap<String, Object>(nGTKeys - 1);
 
                 for (int i = 0; i < nGTKeys; i++) {
                     final String gtKey = new String(genotypeKeyArray[i]);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 42ea05355..58dfd3589 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -168,7 +168,7 @@ public class VCFCodec extends AbstractVCFCodec {
 
             double GTQual = VariantContext.NO_NEG_LOG_10PERROR;
             Set<String> genotypeFilters = null;
-            Map<String, String> gtAttributes = null;
+            Map<String, Object> gtAttributes = null;
             String sampleName = sampleNameIterator.next();
 
             // check to see if the value list is longer than the key list, which is a problem
@@ -177,7 +177,7 @@ public class VCFCodec extends AbstractVCFCodec {
 
             int genotypeAlleleLocation = -1;
             if (nGTKeys >= 1) {
-                gtAttributes = new HashMap<String, String>(nGTKeys - 1);
+                gtAttributes = new HashMap<String, Object>(nGTKeys - 1);
 
                 for (int i = 0; i < nGTKeys; i++) {
                     final String gtKey = new String(genotypeKeyArray[i]);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index e2e44e2b9..c59c002f2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -25,11 +25,11 @@ public class Genotype {
     protected boolean isPhased = false;
     protected boolean filtersWereAppliedToContext;
 
-    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased) {
         this(sampleName, alleles, negLog10PError, filters, attributes, isPhased, null);
     }
 
-    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased, double[] log10Likelihoods) {
         if ( alleles != null )
             this.alleles = Collections.unmodifiableList(alleles);
         commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
index bf16cd1cf..e7d9b3338 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
@@ -22,22 +22,14 @@ public final class InferredGeneticContext {
     private Set<String> filters = NO_FILTERS;
     private Map<String, Object> attributes = NO_ATTRIBUTES;
 
-//    public InferredGeneticContext(String name) {
-//        this.name = name;
-//    }
-//
-//    public InferredGeneticContext(String name, double negLog10PError) {
-//        this(name);
-//        setNegLog10PError(negLog10PError);
-//    }
-
-    public InferredGeneticContext(String name, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public InferredGeneticContext(String name, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         this.name = name;
         setNegLog10PError(negLog10PError);
-        if ( filters != null )
-            setFilters(filters);
-        if ( attributes != null )
-            setAttributes(attributes);
+        if ( filters != null && ! filters.isEmpty() )
+            this.filters = filters;
+        if ( attributes != null && ! attributes.isEmpty() ) {
+            this.attributes = attributes;
+        }
     }
 
     /**
@@ -157,7 +149,7 @@ public final class InferredGeneticContext {
 
         if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable
             attributes = new HashMap<String, Object>();
-        
+
         attributes.put(key, value);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java
index 14419a2a0..fdffb1e10 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java
@@ -17,7 +17,7 @@ public class MutableGenotype extends Genotype {
     }
 
 
-    public MutableGenotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesArePhased) {
+    public MutableGenotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, boolean genotypesArePhased) {
         super(sampleName, alleles, negLog10PError, filters, attributes, genotypesArePhased);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
index a752f4a1b..d563c5180 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
@@ -18,11 +18,11 @@ public class MutableVariantContext extends VariantContext {
     //
     // ---------------------------------------------------------------------------------------------------------
 
-    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
     }
 
-    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
     }
 
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 f52a7087b..ba96b13d8 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -222,7 +222,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @param attributes      attributes
      * @param referenceBaseForIndel   padded reference base
      */
-    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) {
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
         this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false);
     }
 
@@ -239,7 +239,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @param filters         filters: use null for unfiltered and empty set for passes filters
      * @param attributes      attributes
      */
-    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false);
     }
 
@@ -260,7 +260,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @param attributes      attributes
      * @param referenceBaseForIndel   padded reference base
      */
-    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) {
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
         this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, referenceBaseForIndel, true);
     }
 
@@ -277,7 +277,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @param filters        filters: use null for unfiltered and empty set for passes filters
      * @param attributes     attributes
      */
-    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         this(source, contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes, null, false);
     }
 
@@ -334,7 +334,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      */
     private VariantContext(String source, String contig, long start, long stop,
                            Collection<Allele> alleles, Map<String, Genotype> genotypes,
-                           double negLog10PError, Set<String> filters, Map<String, ?> attributes,
+                           double negLog10PError, Set<String> filters, Map<String, Object> attributes,
                            Byte referenceBaseForIndel, boolean genotypesAreUnparsed) {
         if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
         this.contig = contig;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 43f91041f..0bb01dbb5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -69,7 +69,7 @@ public class VariantContextUtils {
      * @param attributes      attributes
      * @return VariantContext object
      */
-    public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+    public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
         return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes != null ? VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index 35c6a4993..ea06d897e 100644
--- a/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -120,7 +120,7 @@ public class VCFWriterUnitTest extends BaseTest {
         GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1",1);
         List<Allele> alleles = new ArrayList<Allele>();
         Set<String> filters = null;
-        Map<String, String> attributes = new HashMap<String,String>();
+        Map<String, Object> attributes = new HashMap<String,Object>();
         Map<String, Genotype> genotypes = new HashMap<String,Genotype>();
 
         alleles.add(Allele.create("-",true));
@@ -128,7 +128,7 @@ public class VCFWriterUnitTest extends BaseTest {
 
         attributes.put("DP","50");
         for (String name : header.getGenotypeSamples()) {
-            Map<String, String> gtattributes = new HashMap<String,String>();
+            Map<String, Object> gtattributes = new HashMap<String,Object>();
             gtattributes.put("BB","1");
             Genotype gt = new Genotype(name,alleles.subList(1,2),0,null,gtattributes,true);