diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java
index 2fc64a4d0..4f832b8ae 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.contexts;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.genotype.Genotype;
-import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.gatk.refdata.*;
 
 import java.util.*;
 import org.apache.commons.jexl.*;
@@ -11,159 +11,305 @@ import org.apache.commons.jexl.*;
 /**
  * @author ebanks
  *         <p/>
- *         Interface VariantContext
+ *         Class VariantContext
  *         <p/>
  *         This class represents a context that unifies one or more variants
  */
-public interface VariantContext {
+public class VariantContext {
+
+    private static final String UNIQUIFIED_SUFFIX = ".unique";
+
+    private Set<Allele> alleles;
+
+    private Set<Genotype> genotypes;
+
+    private Allele reference;
+
+    private GenomeLoc loc;
+
+    private HashMap<Object, Object> attributes;
+
+
+    public VariantContext(VariationRod rod) {
+
+        // TODO -- VariationRod should eventually require classes to implement toVariationContext()
+        // TODO --  (instead of using a temporary adapter class)
+
+        loc = rod.getLocation();
+        reference = new Allele(Allele.AlleleType.REFERENCE, rod.getReference());
+
+        // TODO -- populate the alleles and genotypes through an adapter
+        alleles = new HashSet<Allele>();
+        genotypes = new HashSet<Genotype>();
+
+        attributes = new HashMap<Object, Object>();
+    }
+
+    protected VariantContext(GenomeLoc loc, Allele reference, Set<Allele> alleles, Set<Genotype> genotypes, HashMap<Object, Object> attributes) {
+        this.loc = loc;
+        this.reference = reference;
+        this.alleles = new HashSet<Allele>(alleles);
+        this.genotypes = new HashSet<Genotype>(genotypes);
+        this.attributes = new HashMap<Object, Object>(attributes);
+    }
+
+    /**
+     * @param other  another variant context
+     *
+     * throws an exception if there is a collision such that the same sample exists in both contexts
+     * @return a context representing the merge of this context and the other provided context
+     */
+    public VariantContext merge(VariantContext other) {
+        return merge(other, false);
+    }
+
+    /**
+     * @param other            another variant context
+     * @param uniquifySamples  if true and there is a collision such that the same sample exists in both contexts,
+     *                           the samples will be uniquified(based on their sources);
+     *                           otherwise, an exception will be thrown
+     *
+     * @return a context representing the merge of this context and the other provided context
+     */
+    public VariantContext merge(VariantContext other, boolean uniquifySamples) {
+        if ( !loc.equals(other.getLocation()) )
+            throw new IllegalArgumentException("The locations must be identical for two contexts to be merged");
+
+        Set<String> samples = getSampleNames();
+        Set<Genotype> Gs = new HashSet<Genotype>(genotypes);
+
+        for ( Genotype g : other.getGenotypes() ) {
+            if ( samples.contains(g.getSample()) ) {
+                if ( uniquifySamples )
+                    g.setSample(g.getSample() + UNIQUIFIED_SUFFIX);
+                else
+                    throw new IllegalStateException("The same sample name exists in both contexts when attempting to merge");
+            }
+            Gs.add(g);
+        }
+
+        HashMap<Object, Object> attrs = new HashMap<Object, Object>(attributes);
+        attrs.putAll(other.getAttributes());
+
+        return createNewContext(Gs, attrs);
+    }
 
     /**
      * @return the location of this context
      */
-    public GenomeLoc getLocation();
+    public GenomeLoc getLocation() { return loc; }
 
     /**
-     * @return the reference base or bases for this context, as a string
+     * @return the reference allele for this context
      */
-    public String getReference();
+    public Allele getReference() { return reference; }
 
     /**
      * @return true if the context is variant (i.e. contains a non-reference allele)
      */
-    public boolean isVariant();
+    public boolean isVariant() {
+        for ( Allele allele : alleles ) {
+            if ( allele.isVariant() )
+                return true;
+        }
+        return false;
+    }
 
     /**
      * @return true if the context is strictly bi-allelic
      */
-    public boolean isBiallelic();
+    public boolean isBiallelic() {
+        return getAlternateAlleles().size() == 1;
+    }
 
     /**
-     * @return true if the context represents point mutations only (i.e. no indels or structural variants)
+     * @return true if the context represents point alleles only (i.e. no indels or structural variants)
      */
-    public boolean isPointMutation();
+    public boolean isPointAllele() {
+        for ( Allele allele : alleles ) {
+            if ( allele.isVariant() && !allele.isSNP() )
+                return false;
+        }
+        return true;
+    }
 
     /**
-     * @param sample  the sample name
-     *
-     * @return true if the context contains data for the given sample
+     * @return the set of all sample names in this context
      */
-    public boolean hasSample(String sample);
-
-    /**
-     * @param sample  the sample name
-     *
-     * @return true if the context contains data for only a single instance of the given sample
-     */
-    public boolean hasSingleInstanceOfSample(String sample);
-
-    /**
-     * @return the number of samples in this context.
-     *      If a given sample has more than one instance in this context, each one is counted separately
-     */
-    public int size();
-
-    /**
-     * @return the number of unique samples in this context
-     */
-    public int numSamples();
-
-    /**
-     * @return the set of all unique sample names in this context
-     */
-    public Set<String> getSampleNames();
+    public Set<String> getSampleNames() {
+        Set<String> samples = new TreeSet<String>();
+        for ( Genotype g : genotypes )
+            samples.add(g.getSample());
+        return samples;
+    }
 
     /**
      * @return true if the context represents variants with associated genotypes
      */
-    public boolean hasGenotypes();
+    public boolean hasGenotypes() { return genotypes.size() > 0; }
 
     /**
      * @return set of all Genotypes associated with this context
      */
-    public Set<Genotype> getGenotypes();
-
-    /**
-     * @param sample  the sample name
-     *
-     * @return set of all Genotypes associated with the given sample in this context
-     */
-    public Set<Genotype> getGenotypes(String sample);
+    public Set<Genotype> getGenotypes() { return genotypes; }
 
     /**
      * @param sample  the sample name
      *
      * @return the Genotype associated with the given sample in this context or null if the sample is not in this context
-     *     throws an exception if multiple instances of the sample exist in the context
      */
-    public Genotype getGenotype(String sample);    
-
-    /**
-     * @param sample  the sample name
-     *
-     * @return the Variation associated with the given sample in this context or null if the sample is not in this context
-     */
-    public Variation toVariation(String sample);
+    public Genotype getGenotype(String sample) {
+        for ( Genotype g : genotypes ) {
+            if ( g.getSample().equals(sample) )
+                return g;
+        }
+        return null;
+    }
 
     /**
      * @return set of all subclasses within this context
      */
-    public Set<String> getSubclasses();
+    public Set<Object> getSubclasses() {
+        Set<Object> subclasses = new HashSet<Object>();
+        for ( Genotype g : genotypes )
+            subclasses.addAll(g.getAttributes().keySet());
+        return subclasses;
+    }
 
     /**
      * @param subclass  the name of a subclass of variants to select
      *
      * @return a subset of this context which selects based on the given subclass
      */
-    public VariantContext select(String subclass);
+    public VariantContext select(String subclass) {
+        HashSet<Genotype> Gs = new HashSet<Genotype>();
+        for ( Genotype g : genotypes ) {
+            if ( g.getAttribute(subclass) != null )
+                Gs.add(g);
+        }
+        return createNewContext(Gs, attributes);
+    }
 
     /**
      * @param expr  a jexl expression describing how to filter this context
      *
      * @return a subset of this context which is filtered based on the given expression
      */
-    public VariantContext filter(String expr);
+    public VariantContext filter(String expr) {
+        HashSet<Genotype> Gs = new HashSet<Genotype>();
+        try {
+            Expression filterExpression = ExpressionFactory.createExpression(expr);
+
+            for ( Genotype g : genotypes ) {
+                JexlContext jContext = JexlHelper.createContext();
+                jContext.setVars(g.getAttributes());
+                if ( (Boolean)filterExpression.evaluate(jContext) )
+                    Gs.add(g);
+            }
+
+        } catch (Exception e) {
+            throw new StingException("JEXL error in VariantContext: " + e.getMessage());
+        }
+
+        return createNewContext(Gs, attributes);
+    }
 
     /**
-     * @return a set of variant contexts where each one represents (all instances of) a single sample from this context
+     * @return a set of new variant contexts, one for each sample from this context
      */
-    public Set<VariantContext> splitBySample();
+    public Set<VariantContext> splitBySample() {
+        Set<VariantContext> contexts = new HashSet<VariantContext>();
+        for ( Genotype g : genotypes ) {
+            HashSet<Genotype> gAsSet = new HashSet<Genotype>();
+            gAsSet.add(g);
+            contexts.add(createNewContext(gAsSet, attributes));
+        }
+        return contexts;
+    }
 
     /**
-     * get the alternate allele frequency of this variant context, if the context is variable.
-     * If this context is not variable or a frequency cannot be provided, this method should return 0.
+     * @param Gs    the set of genotypes from which to create a new context
+     * @param attrs the attributes for the new context
      *
-     * WARNING: This method is valid only for bi-allelic contexts; the contract is to check isBiallelic()
-     * before calling this method
-     *
-     * @return double the minor allele frequency
+     * @return a new context based on the given genotypes
      */
-    public double getNonRefAlleleFrequency();
+    private VariantContext createNewContext(Set<Genotype> Gs, HashMap<Object, Object> attrs) {
+        HashSet<Allele> As = new HashSet<Allele>();
+        for ( Genotype g : Gs )
+            As.addAll(g.getAlleles());
+        return new VariantContext(loc, reference, As, Gs, attrs);
+    }
 
     /**
-     * get the -1 * (log 10 of the error value)
+     * @param allele  the allele to be queried
      *
-     * @return the postive number space log based error estimate
+     * @return the frequency of the given allele in this context
      */
-    public double getNegLog10PError();
+    public double getAlleleFrequency(Allele allele) {
+
+        int alleleCount = 0;
+        int totalCount = 0;
+
+        for ( Genotype g : genotypes ) {
+            for ( Allele a : g.getAlleles() ) {
+                totalCount++;
+                if ( allele.equals(a) )
+                    alleleCount++;
+            }
+        }
+
+        return totalCount == 0 ? 0.0 : (double)alleleCount / (double)totalCount;
+    }
 
     /**
-     * gets the alleles.  This method should return all of the alleles present at the location,
-     * including the reference base.  The first allele should always be the reference allele, followed
-     * by an unordered list of alternate alleles. If the reference base is not an allele in this varation
-     * it will not be in the list (i.e. there is no guarantee that the reference base is in the list).
+     * Gets the alleles.  This method should return all of the alleles present at the location,
+     * including the reference allele.  There are no constraints imposed on the ordering of alleles
+     * in the set. If the reference is not an allele in this context it will not be included.
      *
-     * @return an alternate allele list
+     * @return the set of alleles
      */
-    public List<String> getAlleles();
+    public Set<Allele> getAlleles() { return alleles; }
 
     /**
-     * gets the alternate alleles.  This method should return all the alleles present at the location,
-     * NOT including the reference base.  This is returned as a string list with no guarantee ordering
-     * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
-     * frequency).
+     * Gets the alternate alleles.  This method should return all the alleles present at the location,
+     * NOT including the reference allele.  There are no constraints imposed on the ordering of alleles
+     * in the set.
      *
-     * @return an alternate allele list
+     * @return the set of alternate alleles
      */
-    public List<String> getAlternateAlleleList();
+    public Set<Allele> getAlternateAlleles() {
+        HashSet<Allele> altAlleles = new HashSet<Allele>();
+        for ( Allele allele : alleles ) {
+            if ( !allele.equals(reference) )
+                altAlleles.add(allele);
+        }
+        return altAlleles;
+    }
+
+    /**
+     * Sets the given attribute
+     *
+     * @param key    the attribute key
+     * @param value  the attribute value
+     */
+    public void setAttribute(Object key, Object value) {
+        attributes.put(key, value);
+    }
+
+    /**
+     * @param key    the attribute key
+     *
+     * @return the attribute value for the given key (or null if not set)
+     */
+    public Object getAttribute(Object key) {
+        return attributes.get(key);
+    }
+
+    /**
+     * @return the attribute map
+     */
+    public Map<Object, Object> getAttributes() {
+        return attributes;
+    }
 
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Allele.java b/java/src/org/broadinstitute/sting/gatk/refdata/Allele.java
new file mode 100755
index 000000000..4c00af667
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Allele.java
@@ -0,0 +1,79 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class Allele
+ *         <p/>
+ *         This class emcompasses all the basic information about an allele
+ */
+public class Allele {
+
+    private AlleleType type;
+
+    private String bases;
+
+
+    // the types of variants we currently allow
+    public enum AlleleType {
+        REFERENCE, SNP, INSERTION, DELETION, INVERSION
+    }
+
+    public Allele(AlleleType type, String bases) {
+        this.type = type;
+        if ( bases == null )
+            throw new IllegalArgumentException("Constructor: the Allele base string cannot be null");
+        if ( type == AlleleType.DELETION && bases.length() > 0 )
+            throw new IllegalArgumentException("Constructor: deletions cannot have observed bases");
+        this.bases = bases.toUpperCase();
+    }
+
+    /**
+     * convenience method for switching over the allele type
+     *
+     * @return the AlleleType of this allele
+     **/
+    public AlleleType getType() { return type; }
+
+    /**
+     * convenience method for SNPs
+     *
+     * @return true if this is a SNP, false otherwise
+     */
+    public boolean isSNP() { return type == AlleleType.SNP; }
+
+    /**
+     * convenience method for variants
+     *
+     * @return true if this is a variant allele, false if it's reference
+     */
+    public boolean isVariant() { return type != AlleleType.REFERENCE; }
+
+
+    /**
+     * convenience method for indels
+     *
+     * @return true if this is an indel, false otherwise
+     */
+    public boolean isIndel() { return type == AlleleType.INSERTION || type == AlleleType.DELETION; }
+
+
+    /**
+     * For deletions, this method returns an empty String.
+     * For everything else, observed bases for the allele are returned.
+     *
+     * @return the bases, as a string
+     */
+    public String getBases() { return bases; }
+
+    /**
+     * @param other  the other allele
+     *
+     * @return true if these alleles are equal
+     */
+    public boolean equals(Allele other) {
+        return type == other.getType() && bases.equals(other.getBases());
+    }
+
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
old mode 100644
new mode 100755
index 41aa1e0b9..ace9cda35
--- a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
@@ -1,172 +1,147 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: asivache
- * Date: Apr 1, 2009
- * Time: 11:02:03 AM
- * To change this template use File | Settings | File Templates.
- */
-@Deprecated
-public interface Genotype extends Comparable<ReferenceOrderedDatum> {
-    // ----------------------------------------------------------------------
-    //
-    // manipulating the SNP information
-    //
-    // ----------------------------------------------------------------------
-    /** Location of this genotype on the reference (on the forward strand). If the allele is insertion/deletion, the first inserted/deleted base
-     *  is located right <i>after</i> the specified location
-     *
-     * @return position on the genome wrapped in GenomeLoc object
-     */
-    GenomeLoc getLocation();
-
-    /** Returns actual observed alleles on the fwd strand. Allowed to return more than two alleles (@see #getPloidy()). 
-     * For point genotypes (those that report themselves as isPointGenotype()), the alleles are observed bases. For indels
-     * (i.e. if isIndelGenotype() is true), a no-event allele is represented by an empty string, 
-     * while the event allele is represented by '+' (insertion) or '-' (deletion) followed by actual inserted or deleted bases. 
-     * @return list of alleles
-     */
-    List<String> getFWDAlleles() ;
-
-    
-    /** Returns bases on the fwd strand in the true reference allele (regardless of whether the reference allele 
-     * was observed at this site in this particular genotype!) 
-     * as a String. String can be empty (if alt allele is insertion into
-     * the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
-     * (if alt is a longer deletion). For the actually observed alleles, see #getFWDAlleles()
-     *
-     * @return reference allele, forward strand
-     */
-    String getFWDRefBases();
-    
-    /** Returns reference base (regardless of whether the reference allele was actually observed. This method 
-     * is similar to getFWDRefBases() except it returns a single char. For non-point variants (i.e. indels), behavior
-     * of this method is not specified and can be defined by implementing classes.
-     * @return
-     */
-    char getRef() ;
-
-    /** Returns true if the object represents a point genotype (e.g. reference base vs. a SNP),
-     * regardless of what the actual observation is (see isReference() and isSNP()).
-     * @return
-     */
-    boolean isPointGenotype() ;
-    
-    /** Returns true if the object represents an extended (indel) genotype (e.g. insertion/deletion event vs. no event),
-     * regardless of what the actual observation is (see isReference(), isIndel(), isInsertion(), isDeletion()).
-     * @return
-     */
-    boolean isIndelGenotype() ;
-
-    
-    /** Is this variant a SNP? Returns true only if this is point genotype AND a non-reference base was observed, false otherwise.
-    *
-    * @return true or false
-    */
-   boolean isSNP();
-
-   /** Returns true if all observed alleles are reference ones (only reference base was observed if this is a point genotype,
-    * or no indel events were observed if this is an indel genotype). All is"Variant" methods (where Variant=SNP,Insertion, etc) should
-    * return false at a site where isReference() is true to ensure consistency. 
-    * @return
-    */
-   boolean isReference();
-
-   
-   /** Is this variant an insertion? Returns true if this is indel genotype AND only insertion event(s) was observed,
-    * false otherwise. The contract requires isIndel() to return true
-    * whenever isInsertion() method returns true.
-    *
-    * @return true or false
-    */
-   boolean isInsertion();
-
-   
-   /** Is this variant a deletion? Returns true if this is indel genotype AND only deletion event(s) was observed,
-    * false otherwise. The contract requires isIndel() to return true
-    * whenever isDeletion() method returns true.
-    *
-    * @return true or false
-    */
-   boolean isDeletion();
-
-  
-   /** Is this variant an insertion or a deletion? The contract requires
-    * this to be true if either isInsertion() or isDeletion() returns true. However,
-    * this method is also allowed to return true even if neither isInsertion()
-    * nor isDeletion() do (e.g. a het genotype with one insertion and one deletion). Always returns
-    * false if the object does not represent indel genotype. 
-    * @return
-    */
-   boolean isIndel();
-  
-   
-   /** Returns phred-scaled confidence for the variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
-   *
-   * @return
-   */
-  double getVariantConfidence();
-
-  /** Returns phred-mapped confidence in called genotype (e.g. MAQ's consensus confidence, or AlleleCaller's
-   * best vs next-best.
-   * @return
-   */
-  double getConsensusConfidence();
-
-
-  /** Returns true if the site has at most two known or observed alleles (ref and non-ref), or false if there are > 2 allelic variants known or observed. When
-   * the implementing class is a genotype, alleles should be always counted including the reference allele whether it was observed in the particular
-   * individual or not: i.e. if the reference is 'C', then both 'CA' and 'AA' genotypes must be reported as bi-allelic, while 'AT' is <i>not</i> bi-allelic (since there are
-   * two allelic variants, 'A' and 'T' <i>in addition</i> to the (known) reference variant 'C'). 
-   * @return
-   */
-  boolean isBiallelic() ;
-  
-  /** Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
-   *  
-   * @return
-   */
-  boolean isHom() ;
-
-  /** Returns true if observed alleles differ (regardless of whether they are ref or alt)
-   *  
-   * @return
-   */
-  boolean isHet() ;
-
-  /** Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
-     * if variant is not a SNP.
-     *
-     * @return reference base on the forward strand
-     */
-    //char getRefSnpFWD() throws IllegalStateException;
-
-    /** Returns bases in the alternative allele as a String. String can be empty (as in deletion from
-     * the reference), can contain a single character (as in SNP or one-base insertion), or multiple characters
-     * (for longer indels).
-     *
-     * @return alternative allele, forward strand
-     */
-    //String getAltBasesFWD();
-
-    /** Returns alternative (minor) allele base for a SNP variant as a character; should throw IllegalStateException
-     * if variant is not a SNP.
-     *
-     * @return alternative allele base on the forward starnd
-     */
-  //  char getAltSnpFWD() throws IllegalStateException;
-    
-  int length();
-
-
-    /** Return actual number of observed alleles (chromosomes) in the genotype.
-     * @return
-     */
-//    int getPloidy() throws IllegalStateException;
-    
- }
+package org.broadinstitute.sting.gatk.refdata;
+
+import java.util.*;
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class Genotype
+ *         <p/>
+ *         This class emcompasses all the basic information about a genotype
+ */
+public class Genotype {
+
+    private List<Allele> alleles;
+
+    private double negLog10PError;
+
+    private String sample;
+
+    private HashMap<Object, Object> attributes;
+
+
+    public Genotype(List<Allele> alleles, String sample, double negLog10PError) {
+        this.alleles = new ArrayList<Allele>(alleles);
+        this.sample = sample;
+        this.negLog10PError = negLog10PError;
+        attributes = new HashMap<Object, Object>();
+    }
+
+    /**
+      * @return the alleles for this genotype
+      */
+     public List<Allele> getAlleles() { return alleles; }
+
+    /**
+     * @return the ploidy of this genotype
+     */
+    public int getPloidy() { return alleles.size(); }
+
+    /**
+     * @return true if all observed alleles are the same (regardless of whether they are ref or alt)
+     */
+    public boolean isHom() {
+
+        // do not assume ploidy == 2
+
+        if ( alleles.size() == 0 )
+            return true;
+
+        Allele first = alleles.get(0);
+        for ( int i = 1; i < alleles.size(); i++ ) {
+            if ( !first.equals(alleles.get(i)) )
+                return false;
+        }
+
+        return true;
+    }
+
+    /**
+     * @return true if we're het (observed alleles differ)
+     */
+    public boolean isHet() { return !isHom(); }
+
+    /**
+     * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
+     */
+    public boolean isNoCall() {
+        // TODO -- implement me
+        return false;
+    }
+
+    /**
+     * @return true if all alleles for this genotype are SNPs or reference
+     */
+    public boolean isPointGenotype() {
+        for ( Allele allele : alleles ) {
+            if ( allele.isVariant() && !allele.isSNP() )
+                return false;
+        }
+        return true;
+    }
+
+    /**
+     * @return true if this is a variant genotype, false if it's reference
+     */
+    public boolean isVariant() {
+        for ( Allele allele : alleles ) {
+            if ( allele.isVariant() )
+                return true;
+        }
+        return false;
+    }
+
+    /**
+      * @return the -1 * log10-based error estimate
+      */
+    public double getNegLog10PError() { return negLog10PError; }
+
+    /**
+      * @return the sample name
+      */
+    public String getSample() { return sample; }
+
+    /**
+     * Sets the sample name
+     *
+     * @param sample    the sample name
+     */
+    public void setSample(String sample) {
+        this.sample = sample;
+    }
+
+    /**
+     * @param ref the reference base
+     *
+     * @return this genotype as a variation
+     */
+    // TODO -- implement me
+    // public Variation toVariation(char ref);
+
+    /**
+     * Sets the given attribute
+     *
+     * @param key    the attribute key
+     * @param value  the attribute value
+     */
+    public void setAttribute(Object key, Object value) {
+        attributes.put(key, value);
+    }
+
+    /**
+     * @param key    the attribute key
+     *
+     * @return the attribute value for the given key (or null if not set)
+     */
+    public Object getAttribute(Object key) {
+        return attributes.get(key);
+    }
+
+    /**
+     * @return the attribute map
+     */
+    public Map<Object, Object> getAttributes() {
+        return attributes;
+    }
+
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/GenotypeList.java b/java/src/org/broadinstitute/sting/gatk/refdata/GenotypeList.java
deleted file mode 100644
index fd382e277..000000000
--- a/java/src/org/broadinstitute/sting/gatk/refdata/GenotypeList.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-/** A simple wrapper interface that allows for keeping any of the "main" (point mutation) or "associated" (indel)
- * genotypes, or both, at any given reference position. This is the abstraction of "complete" genotyping information:
- * one might have or might have not genotyped independently a base at the given position (point) or an indel right after
- * that position. The query and getter methods allow clients to figure out what pieces of the genotyping information
- * are actually available and to retrieve them. Behavior of the getters when corresponding queries return false is
- * not bound by a contract but it is suggested that they return null or a "trivial" (reference) genotype. 
- * 
- * @author asivache
- *
- */
-
-public interface GenotypeList {
-	/** Returns true if point mutation genotyping information is available at the
-	 * current position.
-	 * @return
-	 */
-	boolean hasPointGenotype();
-
-	/** Returns true if indel genotyping information is available at the
-	 * current position.
-	 * @return
-	 */
-	boolean hasIndelGenotype();
-	
-	/** Returns point mutation genotyping information if available;
-	 * behavior is not specified in the case when there is no such information.
-	 * @return
-	 */
-	Genotype getPointGenotype();
-
-	/** Returns indel genotyping information if available;
-	 * behavior is not specified in the case when there is no such information.
-	 * @return
-	 */
-	Genotype getIndelGenotype();
-	
-	/** Returns position on the reference the stored genotyping data are associated with. 
-	 * 
-	 * @return
-	 */
-	GenomeLoc getLocation();
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
index a84d9268a..6bc7ae95b 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
@@ -29,7 +29,7 @@ import net.sf.samtools.util.StringUtil;
  */
 
 
-public class SAMPileupRecord implements Genotype, GenotypeList {
+public class SAMPileupRecord {
     private static final int NO_VARIANT = -1;
     private static final int SNP_VARIANT = 0;
     private static final int INSERTION_VARIANT = 1;
@@ -428,13 +428,11 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
      *
      * @return reference allele, forward strand
      */
-    @Override
     public String getFWDRefBases() {
         return refBases;
     }
 
         
-    @Override
     public List<String> getFWDAlleles()  {
         return observedAlleles;
     }
@@ -500,34 +498,28 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
     }
     
     
-    @Override
     public double getVariantConfidence() {
         return variantScore;
     }
 
 
-    @Override
     public boolean isBiallelic() {
         return nNonref  < 2;
     }
 
-    @Override
     public double getConsensusConfidence() {
         return consensusScore;
     }
 
-    @Override
     public int length() {
         return eventLength;
     }
 
-	@Override
 	public boolean isIndelGenotype() {
 		return refBaseChar == '*';
 	}
 
 
-	@Override
 	public boolean isPointGenotype() {
 		return ! isIndelGenotype();
 	}
@@ -537,8 +529,7 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 	 * point genotype, this method returns null.
 	 * @return
 	 */
-	@Override
-	public Genotype getIndelGenotype() {
+	public SAMPileupRecord getIndelGenotype() {
 		if ( isIndelGenotype() ) return this;
 		else return null;
 	}
@@ -548,8 +539,7 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 	 * indel genotype, this method returns null.
 	 * @return
 	 */
-	@Override
-	public Genotype getPointGenotype() {
+	public SAMPileupRecord getPointGenotype() {
 		if ( isPointGenotype() ) return this;
 		else return null;
 	}
@@ -558,7 +548,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 	 * indel genotype is what it only has).
 	 * @return
 	 */
-	@Override
 	public boolean hasIndelGenotype() {
 		return isIndelGenotype();
 	}
@@ -567,13 +556,10 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 	 * point genotype is what it only has.
 	 * @return
 	 */
-	@Override
 	public boolean hasPointGenotype() {
 		return isPointGenotype();
 	}
 	
-
-	@Override
 	public int compareTo(ReferenceOrderedDatum o) {
 		return getLocation().compareTo(o.getLocation());
 	}
@@ -596,7 +582,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 			rodName = name;
 		}
 		
-		@Override
 		public boolean hasNext() {
 			return parser.hasNext();
 		}
@@ -605,7 +590,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
          * @return the next element in the iteration.
          * @throws NoSuchElementException - iterator has no more elements.
          */
-		@Override
 		public SAMPileupRecord next() {
              if (!this.hasNext()) throw new NoSuchElementException("SAMPileupRecord next called on iterator with no more elements");
 //			 if ( z == 0 ) t = System.currentTimeMillis();
@@ -621,7 +605,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 		}
 
 
-		@Override
 		public void remove() {
 			throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups");
 		}
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
index 6586c1650..2dbc6b4e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import java.util.Arrays;
 import java.util.List;
 
-public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod {
+public class SimpleIndelROD extends TabularROD implements VariationRod {
 
     private boolean KGENOMES_FORMAT = false, checkedFormat = false;
 
@@ -24,7 +24,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return the reference base or bases, as a string
      */
-    @Override
     public String getReference() {
         return String.valueOf(getRef());
     }
@@ -53,13 +52,11 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return VariantFrequency with the stored frequency
      */
-    @Override
     public double getNonRefAlleleFrequency() {
         return 0.0;
     }
 
     /** @return the VARIANT_TYPE of the current variant */
-    @Override
     public VARIANT_TYPE getType() {
         return isInsertion() ? VARIANT_TYPE.INSERTION : VARIANT_TYPE.DELETION;
     }
@@ -85,7 +82,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return a char, representing the alternate base
      */
-    @Override
     public char getAlternativeBaseForSNP() {
         return getAltSnpFWD();
     }
@@ -95,7 +91,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return a char, representing the alternate base
      */
-    @Override
     public char getReferenceForSNP() {
         return getRefSnpFWD();
     }
@@ -110,7 +105,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return the log based error estimate
      */
-    @Override
     public double getNegLog10PError() {
         return getVariationConfidence();
     }
@@ -123,7 +117,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return an alternate allele list
      */
-    @Override
     public List<String> getAlternateAlleleList() {
         List<String> ret = getAlleleList();
         for (String val : ret) {
@@ -139,7 +132,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
      *
      * @return an alternate allele list
      */
-    @Override
     public List<String> getAlleleList() {
         return this.getFWDAlleles();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
index 33723c165..8ab9c7f88 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
@@ -30,7 +30,7 @@ import net.sf.picard.reference.ReferenceSequenceFileWalker;
 
 
 
-public class rodSAMPileup extends BasicReferenceOrderedDatum implements GenotypeList {
+public class rodSAMPileup extends BasicReferenceOrderedDatum {
 	// ----------------------------------------------------------------------
 	//
 	// Constructors
@@ -71,22 +71,18 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 		return b.toString();
 	}
 
-	@Override
-	public Genotype getIndelGenotype() {
+	public SAMPileupRecord getIndelGenotype() {
 		return indelGenotype;
 	}
 
-	@Override
-	public Genotype getPointGenotype() {
+	public SAMPileupRecord getPointGenotype() {
 		return pointGenotype;
 	}
 
-	@Override
 	public boolean hasIndelGenotype() {
 		return indelGenotype != null;
 	}
 
-	@Override
 	public boolean hasPointGenotype() {
 		return pointGenotype != null;
 	}
@@ -108,7 +104,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 			rodName = name;
 		}
 		
-		@Override
 		public boolean hasNext() {
 			return parser.hasNext();
 		}
@@ -117,7 +112,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
          * @return the next element in the iteration.
          * @throws NoSuchElementException - iterator has no more elements.
          */
-		@Override
 		public rodSAMPileup next() {
             if (!this.hasNext()) throw new NoSuchElementException("rodSAMPileup next called on iterator with no more elements");
 			rodSAMPileup result = new rodSAMPileup(rodName);
@@ -170,7 +164,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 		}
 
 
-		@Override
 		public void remove() {
 			throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups");
 		}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
index 01fdb90b7..ab4d6bcfb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@@ -24,7 +24,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
     public boolean CONTINUE_AFTER_AN_ERROR = false;
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        ReadBackedPileup pileup = context.getPileup();
+        ReadBackedPileup pileup = context.getBasePileup();
         SAMPileupRecord truePileup = getTruePileup( tracker );
 
         if ( truePileup == null ) {
@@ -105,9 +105,9 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
             return null;
 
         if( pileup.hasPointGenotype() )
-            return (SAMPileupRecord)pileup.getPointGenotype();
+            return pileup.getPointGenotype();
         else if( pileup.hasIndelGenotype() )
-            return (SAMPileupRecord)pileup.getIndelGenotype();
+            return pileup.getIndelGenotype();
         else
             throw new StingException("Unsupported pileup type: " + pileup);
     }
diff --git a/java/src/org/broadinstitute/sting/utils/GenotypeUtils.java b/java/src/org/broadinstitute/sting/utils/GenotypeUtils.java
deleted file mode 100644
index 818d671bc..000000000
--- a/java/src/org/broadinstitute/sting/utils/GenotypeUtils.java
+++ /dev/null
@@ -1,216 +0,0 @@
-package org.broadinstitute.sting.utils;
-
-import org.broadinstitute.sting.gatk.refdata.Genotype;
-import org.broadinstitute.sting.gatk.refdata.GenotypeList;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.genotype.Variation;
-
-import java.util.Arrays;
-import java.util.List;
-
-/** Holds useful utility methods and auxiliary default classes for working with Genotype objects
- * 
- * @author asivache
- *
- */
-public class GenotypeUtils {
-	
-	public static enum VariantType {
-		POINT, INDEL;
-//		VariantType() {}
-	}
-
-	/** This method accepts rods that implement either Genotype or GenotypeList interface (all others will result in an exception). Variant
-	 * (Genotype object) of the specified type (point mutation or indel) will be extracted from GenotypeList rod if such variant exists, or the rod itself 
-	 * will be typecasted and returned back if it implements Genotype and represents the specified variant type. If the last argument is false, then 
-	 * null will be returned in all other cases. If the last argument is true and either a) rod is a GenotypeList that lacks a call of the specified type, but call
-	 * of the other type was made, or b) rod is a Genotype and its type is difference from variant_type, then it will be assumed that the implicit ref/ref call
-	 * of the specified type also exists at this genomic position, and new object representing such default call will be returned. If rod argument
-	 * is null, then this method safely (and silently) returns null.
-	 *  
-	 * @param rod GenotypeList or Genotype to extract requested call from/upgrade to requested call
-	 * @param variant_type type of the variant to extract (POINT mutations or INDEL)
-	 * @param assume_implicit_ref_calls true if presence of only a call of different type means that ref/ref call of the requested type is implicitly present 
-	 * @return Genotyping call of the requested type or null if no explicit or implicit call was made.
-	 */
-	public static Genotype extractGenotype(ReferenceOrderedDatum rod, VariantType variant_type, boolean assume_implicit_ref_calls) {
-		
-		if ( rod == null ) return null;
-
-		if ( rod instanceof GenotypeList ) {
-
-			GenotypeList rod_gl = (GenotypeList)rod;
-			switch ( variant_type ) {
-			case POINT :
-				if ( rod_gl.hasPointGenotype() ) return rod_gl.getPointGenotype();
-				else {
-					if ( assume_implicit_ref_calls && rod_gl.hasIndelGenotype() ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
-					else return null;
-				}
-			case INDEL:				
-				if ( rod_gl.hasIndelGenotype() ) return rod_gl.getIndelGenotype();
-				else {
-					if ( assume_implicit_ref_calls && rod_gl.hasPointGenotype() ) return new DefaultIndelGenotype(rod_gl.getLocation());
-					else return null;
-				}
-			default: throw new StingException("Unrecognized variant type: "+variant_type);
-			}
-			
-		}	else if ( rod instanceof Genotype ) {
-			
-			Genotype rod_g = (Genotype)rod;
-			switch ( variant_type ) {
-			case POINT:
-				if ( rod_g.isIndelGenotype() ) {
-					if ( assume_implicit_ref_calls  ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
-					else return null;
-				}	else return rod_g;
-			case INDEL: 
-				if ( rod_g.isPointGenotype() ) {
-					if ( assume_implicit_ref_calls  ) return new DefaultIndelGenotype(rod_g.getLocation());
-					else return null;
-				}	else return rod_g;
-			default: throw new StingException("Unrecognized variant type: "+variant_type);
-			} 
-			
-		}
-		else throw new StingException("track "+rod.getName()+" is not a Genotype or GenotypeList");
-	}
-
-    public static boolean isHet(Variation var) {
-        if ( var instanceof Genotype )
-            return ((Genotype)var).isHet();
-
-        String genotype = Utils.join("",var.getAlleleList());
-        if ( genotype.length() < 1 )
-            return false;
-
-        char first = genotype.charAt(0);
-        for (char base : genotype.toCharArray()) {
-            if (base != first) return true;
-        }
-        return false;
-    }
-
-	/** This class represents a "default" indel-type genotype with homozygous reference (i.e. confidently no indel)
-	 * call. All the interface methods are implemented and return consistent values. Use this class when working with
-	 * genotyping data where absence of explicit indel call actually means that no evidence for an indel was observed 
-	 *  (SAM pileup is one such example).
-	 * @author asivache
-	 *
-	 */
-	public static class DefaultIndelGenotype implements Genotype {
-		private GenomeLoc location;
-		private static final List<String> alleles = Arrays.asList("","") ;
-		private int confidence ;
-
-		/** Creates default indel genotype (ref/ref = no indel) at the specified position
-		 * with default consensus confidence of 1000 (variant confidence is 0).
-		 * @param l reference position to associate the genotyping call with
-		 */
-		public DefaultIndelGenotype(GenomeLoc l) {
-			this(l,1000);
-		}
-		
-		/** Creates ref/ref (i.e. absense of indel) indel genotype at the specified position
-		 * with the specified consensus confidence (variant confidence is 0).
-		 * @param l reference position to associate the genotyping call with
-		 */
-		public DefaultIndelGenotype(GenomeLoc l, int confidence) {
-			location = l;
-			this.confidence = confidence;
-		}
-
-		@Override
-		public double getConsensusConfidence() {
-			return confidence;
-		}
-
-		@Override
-		public List<String> getFWDAlleles() {
-			return alleles;
-		}
-
-		@Override
-		public String getFWDRefBases() {
-			return alleles.get(0);
-		}
-
-		@Override
-		public GenomeLoc getLocation() {
-			return location;
-		}
-
-		@Override
-		public char getRef() {
-			return '*';
-		}
-
-		@Override
-		public double getVariantConfidence() {
-			return 0.0;
-		}
-
-		@Override
-		public boolean isBiallelic() {
-			return false;
-		}
-
-		@Override
-		public boolean isDeletion() {
-			return false;
-		}
-
-		@Override
-		public boolean isHet() {
-			return false;
-		}
-
-		@Override
-		public boolean isHom() {
-			return true;
-		}
-
-		@Override
-		public boolean isIndel() {
-			return false;
-		}
-
-		@Override
-		public boolean isIndelGenotype() {
-			return true;
-		}
-
-		@Override
-		public boolean isInsertion() {
-			return false;
-		}
-
-		@Override
-		public boolean isPointGenotype() {
-			return false;
-		}
-
-		@Override
-		public boolean isReference() {
-			return true;
-		}
-
-		@Override
-		public boolean isSNP() {
-			return false;
-		}
-
-        @Override
-        public int length() {
-            return (int)(location.getStop() - location.getStart() + 1);
-        }
-
-		@Override
-		public int compareTo(ReferenceOrderedDatum o) {
-			return location.compareTo(o.getLocation());
-		}
-		
-	}
-
-}
diff --git a/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java b/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java
deleted file mode 100644
index dd018a5d7..000000000
--- a/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.broadinstitute.sting.utils;
-
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.genotype.BasicVariation;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class GenotypeUtilsTest
- *
- * a test class for the various function in the genotype utils class
- */
-public class GenotypeUtilsTest extends BaseTest {
-
-    private static IndexedFastaSequenceFile seq;
-    private static File vcfFile = new File(validationDataLocation + "vcfexample.vcf");
-
-    @BeforeClass
-    public static void beforeTests() {
-        try {
-            seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
-        } catch (FileNotFoundException e) {
-            throw new StingException("unable to load the sequence dictionary");
-        }
-        GenomeLocParser.setupRefContigOrdering(seq);
-
-    }
-
-    /**
-     * make sure that the variation is a het
-     */
-    @Test
-    public void isHetTest() {
-        GenomeLoc loc = GenomeLocParser.createGenomeLoc(0,1,2);
-        BasicVariation var = new BasicVariation("AA", "A", 0, loc,0.0);
-        Assert.assertTrue(!GenotypeUtils.isHet(var));
-        BasicVariation var2 = new BasicVariation("AG", "A", 0, loc,0.0);
-        Assert.assertTrue(GenotypeUtils.isHet(var2));
-        BasicVariation var3 = new BasicVariation("GG", "A", 0, loc,0.0);
-        Assert.assertTrue(!GenotypeUtils.isHet(var3));
-    }
-
-}