From b401929e4145148ed8c291e167b66768ff39141a Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Sep 2009 04:48:42 +0000
Subject: [PATCH] incremental clean-up and changes for VariantEval, moved
 DiploidGenotype to a better home, and fixed a spelling error.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/RodGLF.java            |  20 ++-
 .../sting/gatk/refdata/RodGeliText.java       | 170 ++++++++++--------
 .../gatk/refdata/RodGenotypeChipAsGFF.java    |  30 +++-
 .../sting/gatk/refdata/rodDbSNP.java          |  31 +++-
 .../genotyper/DiploidGenotypePriors.java      |   7 +-
 .../genotyper/GenotypeLikelihoods.java        |   1 +
 .../walkers/genotyper/SSGenotypeCall.java     |   2 +-
 .../gatk/walkers/CoverageEvalWalker.java      |   2 +-
 .../gatk/walkers/HLAcaller/CallHLAWalker.java |   1 +
 .../varianteval/BasicPoolVariantAnalysis.java |   4 +-
 .../varianteval/CallableBasesAnalysis.java    |   7 +-
 .../varianteval/GenotypeConcordance.java      |   2 +-
 .../PooledGenotypeConcordance.java            |   3 +-
 .../TransitionTranversionAnalysis.java        |  12 +-
 .../walkers/varianteval/VariantCounter.java   |   2 +-
 .../varianteval/VariantDBCoverage.java        |  23 +--
 .../varianteval/VariantEvalWalker.java        |  19 +-
 .../walkers/varianteval/VariantMatcher.java   |   3 +-
 .../sting/utils/genotype/BasicGenotype.java   |   2 +-
 .../sting/utils/genotype/BasicVariation.java  |  34 +++-
 .../genotype}/DiploidGenotype.java            |  11 +-
 .../sting/utils/genotype/GenotypesBacked.java |   2 +-
 .../utils/genotype/LikelihoodObject.java      |  14 +-
 .../genotype/VariantBackedByGenotype.java     |  16 +-
 .../sting/utils/genotype/Variation.java       |  12 +-
 .../utils/genotype/geli/GeliTextWriter.java   |   2 +-
 .../sting/utils/genotype/glf/GLFWriter.java   |   3 +-
 .../sting/gatk/refdata/RodGLFTest.java        |   2 +-
 .../genotyper/GenotypeLikelihoodsTest.java    |   6 +-
 .../utils/genotype/DiploidGenotypeTest.java   | 104 +++++++++++
 .../utils/genotype/LikelihoodObjectTest.java  |   6 +-
 31 files changed, 369 insertions(+), 184 deletions(-)
 rename java/src/org/broadinstitute/sting/{gatk/walkers/genotyper => utils/genotype}/DiploidGenotype.java (71%)
 create mode 100644 java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeTest.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
index c0757c348..b3868242a 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
@@ -119,8 +119,8 @@ public class RodGLF implements ReferenceOrderedDatum, Variation, Iterator<RodGLF
      * @return the reference base or bases, as a string
      */
     @Override
-    public char getReference() {
-        return mRecord.getRefBase().toChar();
+    public String getReference() {
+        return mRecord.getRefBase().toString();
     }
 
     /**
@@ -154,12 +154,26 @@ public class RodGLF implements ReferenceOrderedDatum, Variation, Iterator<RodGLF
     @Override
     public char getAlternativeBaseForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if (getAlternateBases().charAt(0) == this.getReference())
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
             return getAlternateBases().charAt(1);
         return getAlternateBases().charAt(0);
 
     }
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
+            return getAlternateBases().charAt(0);
+        return getAlternateBases().charAt(1);
+
+    }
+
     /**
      * Is this variant a SNP?
      *
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
index 886adf379..89e1f0e78 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
@@ -38,7 +38,10 @@ import java.util.Arrays;
 import java.util.List;
 
 public class RodGeliText extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, AllelicVariant {
-    public enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
+    public enum Genotype {
+        AA, AC, AG, AT, CC, CG, CT, GG, GT, TT
+    }
+
     public GenomeLoc loc;
     public char refBase = 'N';
     public int depth;
@@ -47,15 +50,17 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     public double lodBtr;
     public double lodBtnb;
     public double[] genotypeLikelihoods = new double[10];
-    
+
     public RodGeliText(final String name) {
         super(name);
     }
 
-    public String delimiterRegex() { return "\\s+"; }
+    public String delimiterRegex() {
+        return "\\s+";
+    }
 
     public boolean parseLine(Object header, String[] parts) throws IOException {
-        if ( parts.length < 18 )
+        if (parts.length < 18)
             throw new IOException("Invalid rodVariant row found -- too few elements.  Expected 18+, got " + parts.length);
         if (!parts[0].startsWith("#")) {
             loc = GenomeLocParser.createGenomeLoc(parts[0], Long.valueOf(parts[1]));
@@ -78,28 +83,30 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
 
     public String toString() {
         return String.format("%s\t%d\t%c\t%d\t%d\t%s\t%4.4f\t%4.4f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f",
-                loc.getContig(),
-                loc.getStart(),
-                refBase,
-                depth,
-                maxMappingQuality,
-                bestGenotype,
-                lodBtr,
-                lodBtnb,
-                genotypeLikelihoods[0],
-                genotypeLikelihoods[1],
-                genotypeLikelihoods[2],
-                genotypeLikelihoods[3],
-                genotypeLikelihoods[4],
-                genotypeLikelihoods[5],
-                genotypeLikelihoods[6],
-                genotypeLikelihoods[7],
-                genotypeLikelihoods[8],
-                genotypeLikelihoods[9]
+                             loc.getContig(),
+                             loc.getStart(),
+                             refBase,
+                             depth,
+                             maxMappingQuality,
+                             bestGenotype,
+                             lodBtr,
+                             lodBtnb,
+                             genotypeLikelihoods[0],
+                             genotypeLikelihoods[1],
+                             genotypeLikelihoods[2],
+                             genotypeLikelihoods[3],
+                             genotypeLikelihoods[4],
+                             genotypeLikelihoods[5],
+                             genotypeLikelihoods[6],
+                             genotypeLikelihoods[7],
+                             genotypeLikelihoods[8],
+                             genotypeLikelihoods[9]
         );
     }
 
-    public GenomeLoc getLocation() { return loc; }
+    public GenomeLoc getLocation() {
+        return loc;
+    }
 
     /**
      * get the reference base(s) at this position
@@ -107,8 +114,8 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      * @return the reference base or bases, as a string
      */
     @Override
-    public char getReference() {
-        return this.refBase;
+    public String getReference() {
+        return String.valueOf(this.refBase);
     }
 
 
@@ -161,7 +168,9 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     }
 
     public boolean isSNP() {
-        return (!bestGenotype.equals(Utils.dupString(this.getReference(),2)));
+        if (this.getReference().length() == 1)
+            return (!bestGenotype.equals(this.getReference() + this.getReference()));
+        return false;
     }
 
     public boolean isInsertion() {
@@ -195,12 +204,28 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     @Override
     public char getAlternativeBaseForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if(this.bestGenotype.toString().charAt(0) == this.getReference())
+        // we know that if we're a SNP, the reference is a single base
+        if (this.bestGenotype.toString().charAt(0) == getReference().charAt(0))
             return this.bestGenotype.toString().charAt(1);
         return this.bestGenotype.toString().charAt(0);
 
     }
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        if (!isSNP()) throw new IllegalStateException("This site is not a SNP");
+        // we know that if we're a SNP, the reference is a single base
+        if (bestGenotype.toString().charAt(0) != getReference().charAt(0))
+            return bestGenotype.toString().charAt(1);
+        else
+            return bestGenotype.toString().charAt(0);
+    }
+
     public double getMAF() {
         return 0;
     }
@@ -235,21 +260,37 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     }
 
 
-    public int length() { return 1; }
+    public int length() {
+        return 1;
+    }
 
-    public char getReferenceBase() { return refBase; }
+    public char getReferenceBase() {
+        return refBase;
+    }
 
-    public int getPileupDepth() { return depth; }
+    public int getPileupDepth() {
+        return depth;
+    }
 
-    public int getMaxMappingQuality() { return maxMappingQuality; }
+    public int getMaxMappingQuality() {
+        return maxMappingQuality;
+    }
 
-    public String getBestGenotype() { return bestGenotype; }
+    public String getBestGenotype() {
+        return bestGenotype;
+    }
 
-    public double getLodBtr() { return lodBtr; }
+    public double getLodBtr() {
+        return lodBtr;
+    }
 
-    public double getLodBtnb() { return lodBtnb; }
+    public double getLodBtnb() {
+        return lodBtnb;
+    }
 
-    public double[] getGenotypeLikelihoods() { return genotypeLikelihoods; }
+    public double[] getGenotypeLikelihoods() {
+        return genotypeLikelihoods;
+    }
 
     public void adjustLikelihoods(double[] likelihoods) {
         for (int likelihoodIndex = 0; likelihoodIndex < likelihoods.length; likelihoodIndex++) {
@@ -277,7 +318,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
 
         for (int likelihoodIndex = 0; likelihoodIndex < likelihoods.length; likelihoodIndex++) {
             if (refBase == Genotype.values()[likelihoodIndex].toString().charAt(0) &&
-                refBase == Genotype.values()[likelihoodIndex].toString().charAt(1)) {
+                    refBase == Genotype.values()[likelihoodIndex].toString().charAt(1)) {
                 refLikelihood = genotypeLikelihoods[likelihoodIndex];
             }
         }
@@ -287,40 +328,6 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
         this.lodBtnb = (bestLikelihood - nextBestLikelihood);
     }
 
-    /*
-    public String getRefBasesFWD() {
-        char[] b = { getReferenceBase() };
-        return new String( b );
-    }
-
-    public char getRefSnpFWD() throws IllegalStateException { return getReferenceBase(); }
-    public String getAltBasesFWD() { return getBestGenotype(); }
-    public char getAltSnpFWD() throws IllegalStateException {
-        String bases = getBestGenotype();
-        if ( bases.charAt(0) != getRefSnpFWD() )
-            return bases.charAt(0);
-        else
-            return bases.charAt(1);
-
-    }
-    public boolean isReference() { return ! isSNP(); }
-    public boolean isSNP() { return getLodBtr() > 5; }
-    public boolean isInsertion() { return false; }
-    public boolean isDeletion() { return false; }
-    public boolean isIndel() { return false; }
-    public double getMAF() { return 0; }
-    public double getHeterozygosity() { return 0; }
-    public boolean isGenotype() { return true; }
-    public double getVariationConfidence() { return getLodBtr(); }
-    public double getConsensusConfidence() { return getLodBtnb(); }
-    public List<String> getGenotype() throws IllegalStateException {
-        return Arrays.asList(getBestGenotype());
-    }
-     
-    public int getPloidy() throws IllegalStateException { return 2; }
-    public boolean isBiallelic() { return true; }
-    */
-
     /**
      * get the likelihoods
      *
@@ -328,7 +335,24 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      */
     @Override
     public org.broadinstitute.sting.utils.genotype.Genotype getGenotype(DiploidGenotype x) {
-        if (x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
-        return new BasicGenotype(this.getLocation(),this.bestGenotype,this.getRefSnpFWD(),this.getConsensusConfidence());
+        // figure out the best -switch to this
+        /*Integer values[] = Utils.SortPermutation(this.genotypeLikelihoods);
+        int indexThis = x.ordinal(); 
+        int other = (x.toString().equals(Genotype.values()[values[1]])) ? values[9] : values[8];  
+        double lod = (genotypeLikelihoods[indexThis] - genotypeLikelihoods[other]);*/
+        return new BasicGenotype(getLocation(),x.toString(), refBase, lodBtnb);
+    }
+
+    /**
+     * do we have the specified genotype?  not all backedByGenotypes
+     * have all the genotype data.
+     *
+     * @param x the genotype
+     *
+     * @return true if available, false otherwise
+     */
+    @Override
+    public boolean hasGenotype(DiploidGenotype x) {
+        return (x.toString().equals(this.getAltBasesFWD()));
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
index 135c792f3..0f0ad103c 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import java.util.*;
 import java.util.regex.MatchResult;
@@ -82,8 +82,8 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
      * @return the reference base or bases, as a string
      */
     @Override
-    public char getReference() {
-        return 'N';
+    public String getReference() {
+        throw new IllegalStateException("Chip data is unable to determine the reference");
     }
 
     /**
@@ -223,6 +223,16 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
         return this.getAltSnpFWD();
     }
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        return this.getRefSnpFWD();
+    }
+
     public double getMAF() { return 0; }
     public double getHeterozygosity() { return 0; }
     public boolean isGenotype() { return true; }
@@ -247,4 +257,18 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
         if (!x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
         return new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence());
     }
+
+    /**
+     * do we have the specified genotype?  not all backedByGenotypes
+     * have all the genotype data.
+     *
+     * @param x the genotype
+     *
+     * @return true if available, false otherwise
+     */
+    @Override
+    public boolean hasGenotype(DiploidGenotype x) {
+        if (!x.toString().equals(this.getAltBasesFWD())) return false;
+        return true;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index fc5abcc34..16fb7123b 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata;
 import net.sf.picard.util.SequenceUtil;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 import java.util.Arrays;
 import java.util.List;
@@ -68,8 +68,8 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
      * @return the reference base or bases, as a string
      */
     @Override
-    public char getReference() {
-        return getRefSnpFWD();
+    public String getReference() {
+        return getRefBasesFWD();
     }
 
     /**
@@ -183,6 +183,16 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
         return getAlternateBases().charAt(0); */
     }
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        return 0;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
     public boolean isReference()        { return false; } // snp locations are never "reference", there's always a variant
 
     public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
@@ -314,7 +324,20 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
      */
     @Override
     public org.broadinstitute.sting.utils.genotype.Genotype getGenotype(DiploidGenotype x) {
-        if (x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
+        if (!x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
         return new BasicGenotype(this.getLocation(),this.getAltBasesFWD(),this.getRefSnpFWD(),this.getConsensusConfidence());
     }
+
+    /**
+     * do we have the specified genotype?  not all backedByGenotypes
+     * have all the genotype data.
+     *
+     * @param x the genotype
+     *
+     * @return true if available, false otherwise
+     */
+    @Override
+    public boolean hasGenotype(DiploidGenotype x) {
+        return (!x.toString().equals(this.getAltBasesFWD())) ?  false : true;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
index 0fa201970..0973341f4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
@@ -2,15 +2,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
-import static java.lang.Math.log10;
-import static java.lang.Math.pow;
 import java.util.Arrays;
 
-import net.sf.samtools.SAMRecord;
-
 public class DiploidGenotypePriors {
     // --------------------------------------------------------------------------------------------------------------
     //
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index 88b155a1d..fdab218c3 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCall.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCall.java
index 401c5fc3e..be6336c8d 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCall.java
@@ -225,7 +225,7 @@ public class SSGenotypeCall implements Genotype, ReadBacked, GenotypesBacked, Li
      */
     public Variation toVariation() {
         double bestRef = Math.abs(mGenotypeLikelihoods.getPosterior(getBestGenotype()) - mGenotypeLikelihoods.getPosterior(getRefGenotype()));
-        return new BasicVariation(this.getBases(), this.getReference(), 0, this.mLocation, bestRef);
+        return new BasicVariation(this.getBases(), String.valueOf(this.getReference()), 0, this.mLocation, bestRef);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
index 255bcac00..905ee2a68 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.RodGenotypeChipAsGFF;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.SSGenotypeCall;
 import org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.ListUtils;
 import org.broadinstitute.sting.utils.Utils;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
index 844fff653..227e9e3a8 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
@@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.BufferedReader;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java
index 1fd77bd3d..ce1d4732b 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
-import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.PrintStream;
 import java.util.List;
@@ -53,6 +53,6 @@ public abstract class BasicPoolVariantAnalysis implements VariantAnalysis{
         // no need to finalize data in general
     }
 
-    public abstract String update(AllelicVariant variant, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context);
+    public abstract String update(Variation variant, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context);
 
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java
index 5fd2acfba..aa6b7acdc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.Genotype;
@@ -78,13 +78,8 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
                 discoverable_bases[i]++;
             if (!eval.isSNP() && genotype.getNegLog10PError() >= threshold)
                 discoverable_bases[i]++;
-
             if (genotype.getNegLog10PError() >= threshold)
                 genotypable_bases[i]++;
-
-            //System.out.printf("Updating %s SNP=%b, REF=%b VarConf=%f ConConf=%f where threshold=%f: discoverable = %d, genotypable = %d%n",
-            //        eval.getLocation(), eval.isSNP(), eval.isReference(), eval.getVariationConfidence(),
-            //        eval.getConsensusConfidence(), threshold, discoverable_bases[i], genotypable_bases[i]);
         }
 
         return null;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
index ed6d1c15a..c1331a6ef 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
index 18d2bad20..c23d1de68 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java
index 004946854..1e3da6613 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java
@@ -27,21 +27,13 @@ public class TransitionTranversionAnalysis extends BasicVariantAnalysis implemen
 
     public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         if (eval != null && eval.isSNP()) {
-            if (eval.getAlternateBases().length() != 2) {
-                throw new StingException("TransitionTranversionAnalysis works only with biallelic variants");
-            }
-
-
-            char refBase = eval.getReference();
-            char altBase = (eval.getAlternateBases().charAt(0) == refBase) ? eval.getAlternateBases().charAt(1) : eval.getAlternateBases().charAt(0);
-
-            BaseUtils.BaseSubstitutionType subType = BaseUtils.SNPSubstitutionType(refBase, altBase);
+            char altBase = eval.getAlternativeBaseForSNP();
+            BaseUtils.BaseSubstitutionType subType = BaseUtils.SNPSubstitutionType(ref, altBase);
             if (subType == BaseUtils.BaseSubstitutionType.TRANSITION)
                 nTransitions++;
             else
                 nTransversions++;
         }
-
         return null;
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
index 232b2521c..ae1fd211c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
index ef35537d7..36ce49d51 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
@@ -82,27 +82,11 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
     public int nSNPsAtIndels() {
         return nSNPsCalledAtIndels;
     }
-    public static int count = 0;
     public boolean discordantP(Variation dbSNP, Variation eval) {
         if (eval != null) {
-            char alt = (eval.isSNP()) ? eval.getAlternativeBaseForSNP() : eval.getReference();
-
-            if (dbSNP != null && dbSNP.isSNP()) {
-
-                boolean val = !dbSNP.getAlternateBases().contains(String.valueOf(alt));
-
-                if (val) {
-                    //System.err.print(eval.getLocation());
-                    //System.err.print(" eval.alt = " + alt);
-                    //System.err.println(" dbsnp.bases = " + dbSNP.getAlternateBases());
-                    //System.err.println(val);
-
-                    //System.err.println(count);
-                }
-                 //else System.err.println("not count == " + count++);
-
-                return val; 
-            }
+            char alt = (eval.isSNP()) ? eval.getAlternativeBaseForSNP() : eval.getReference().charAt(0);
+            if (dbSNP != null && dbSNP.isSNP())
+                return !dbSNP.getAlternateBases().contains(String.valueOf(alt));
         }
         return false;
     }
@@ -136,7 +120,6 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
                 return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getAlternateBases(), eval);
             } else {
                 return null;
-                // return "Novel      " + eval;
             }
         } else {
             return null;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
index 20d3654d9..4feebb067 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -182,17 +182,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
         // Iterate over each analysis, and update it
         Variation eval = (Variation)tracker.lookup("eval", null);
 
-        //if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ);
-        if ( eval != null ) {
-            // comment to disable variant filtering by confidence score
-            if ( evalContainsGenotypes ) {
-                // Genotyping - use best vs. next best lod
-                if ( eval.getNegLog10PError() < minConfidenceScore ) eval = null;
-            } else {
-                // Variation discovery - use best vs. reference lod
-                if ( Math.abs(eval.getNegLog10PError()) < minConfidenceScore ) eval = null;
-            }
-        }
+        if ( eval != null )
+               if ( eval.getNegLog10PError() < minConfidenceScore ) eval = null;
 
         // update stats about all of the SNPs
         updateAnalysisSet(ALL_SNPS, eval, tracker, ref.getBase(), context);
@@ -204,14 +195,14 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
             updateAnalysisSet(noveltySet, eval, tracker, ref.getBase(), context);
         }
 
-        if ( eval instanceof SNPCallFromGenotypes ) {
+        // are we a population backed call? then update
+        if ( eval instanceof SNPCallFromGenotypes) {
             SNPCallFromGenotypes call = (SNPCallFromGenotypes)eval;
             int nVarGenotypes = call.nHetGenotypes() + call.nHomVarGenotypes();
             //System.out.printf("%d variant genotypes at %s%n", nVarGenotypes, calls);
             final String s = nVarGenotypes == 1 ? SINGLETON_SNPS : TWOHIT_SNPS;
             updateAnalysisSet(s, eval, tracker, ref.getBase(), context);
         }
-
         return 1;
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java
index 14ef39fbe..c831bad37 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.genotype.Variation;
 
@@ -25,7 +24,7 @@ public class VariantMatcher extends BasicVariantAnalysis implements GenotypeAnal
 
     public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         String r = null;
-        AllelicVariant db = (AllelicVariant)tracker.lookup(dbName, null);
+        Variation db = (Variation)tracker.lookup(dbName, null);
         
         if ( eval != null || db != null ) {
             String matchFlag = "    ";
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
index ac295533c..7630acd6a 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
@@ -138,6 +138,6 @@ public class BasicGenotype implements Genotype {
     @Override
     public Variation toVariation() {
         if (!isVariant(this.mRef)) throw new IllegalStateException("this genotype is not a variant");
-        return new BasicVariation(this.getBases(),mRef,this.getBases().length(),mLocation,mNetLog10PError);
+        return new BasicVariation(this.getBases(),String.valueOf(mRef),this.getBases().length(),mLocation,mNetLog10PError);
     }
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java b/java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java
index d258da444..917788749 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 /**
@@ -14,7 +13,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 public class BasicVariation implements Variation {
 
     protected final String mBases;
-    protected final char mRef;
+    protected final String mRef;
     protected final int mLength;
     protected final GenomeLoc mLocation;
     protected final double mConfidence;
@@ -23,11 +22,11 @@ public class BasicVariation implements Variation {
      * the constructor
      *
      * @param bases     the bases that this variant represents
-     * @param reference the reference base
+     * @param reference the reference bases
      * @param length    are we a single base variant, or a indel/deletion? length is negitive for an indel,
      *                  positive for a indel, and 0 for a substitution
      */
-    public BasicVariation(String bases, char reference, int length, GenomeLoc location, double confidence) {
+    public BasicVariation(String bases, String reference, int length, GenomeLoc location, double confidence) {
         mBases = bases;
         mRef = reference;
         mLength = length;
@@ -49,7 +48,7 @@ public class BasicVariation implements Variation {
 
     @Override
     public boolean isSNP() {
-        if (mLength == 0 && Utils.dupString(mRef, 2).equals(mBases)) return true;
+        if (mLength == 0) return true;
         return false;
     }
 
@@ -74,7 +73,7 @@ public class BasicVariation implements Variation {
     }
 
     @Override
-    public char getReference() {
+    public String getReference() {
         return (mRef);
     }
 
@@ -85,8 +84,12 @@ public class BasicVariation implements Variation {
 
     @Override
     public boolean isReference() {
-        if (mLength == 0 && mBases.charAt(0) == mRef && mRef != mBases.charAt(1)) return true;
-        return false;
+        if (mLength != 0) return true;
+        int refIndex = 0;
+        for (char c : mBases.toCharArray()) {
+            if (mRef.charAt(refIndex) != c) return false;
+        }
+        return true;
     }
 
     /**
@@ -108,10 +111,23 @@ public class BasicVariation implements Variation {
     @Override
     public char getAlternativeBaseForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if (getAlternateBases().charAt(0) == this.getReference())
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
             return getAlternateBases().charAt(1);
         return getAlternateBases().charAt(0);
     }
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
+            return getAlternateBases().charAt(0);
+        return getAlternateBases().charAt(1);
+    }
+
 
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
similarity index 71%
rename from java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
rename to java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index 1a6764333..eb5b86ea5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.genotyper;
+package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.Utils;
 
@@ -52,4 +52,13 @@ public enum DiploidGenotype {
             default: return true;
         }
     }
+
+    /**
+     * create a diploid genotype, given a character to make into a hom genotype
+     * @param hom the character to turn into a hom genotype, i.e. if it is A, then returned will be AA
+     * @return the diploid genotype
+     */
+    public static DiploidGenotype createGenotype(char hom) {
+        return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());     
+    }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
index b511a781b..26be15549 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 /**
  * @author aaron
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
index 55b1ae52e..d9d7c3b3b 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
@@ -57,11 +57,11 @@ public class LikelihoodObject {
     // possible types of likihoods to store
 
     public enum LIKELIHOOD_TYPE {
-        NEGITIVE_LOG, LOG, RAW;
+        NEGATIVE_LOG, LOG, RAW;
     }
 
     // our liklihood storage type
-    protected LIKELIHOOD_TYPE mLikelihoodType = LIKELIHOOD_TYPE.NEGITIVE_LOG;
+    protected LIKELIHOOD_TYPE mLikelihoodType = LIKELIHOOD_TYPE.NEGATIVE_LOG;
 
     // default the bestGenotype likelihoods to the allele AA
     protected GENOTYPE bestGenotype = GENOTYPE.AA;
@@ -199,7 +199,7 @@ public class LikelihoodObject {
         double[] ft = toDoubleArray();
         float[] db = new float[ft.length];
         int index = 0;
-        if (this.mLikelihoodType == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
+        if (this.mLikelihoodType == LIKELIHOOD_TYPE.NEGATIVE_LOG) {
             for (; index < ft.length; index++) {
                 db[index] = ((float) ft[index] * -1.0f);
             }
@@ -229,9 +229,9 @@ public class LikelihoodObject {
     public void validateScore(double score) {
         int x = 0;
         switch (mLikelihoodType) {
-            case NEGITIVE_LOG:
+            case NEGATIVE_LOG:
                 if (score < 0)
-                    throw new StingException("Likelikhood score of " + score + " is invalid, for NEGITIVE_LOG it must be greater than or equal to 0");
+                    throw new StingException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0");
                 break;
             case LOG:
                 if (score > 0)
@@ -256,7 +256,7 @@ public class LikelihoodObject {
             return;
         if (mLikelihoodType == LIKELIHOOD_TYPE.RAW) {
             double mult = 1.0;
-            if (likelihood == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
+            if (likelihood == LIKELIHOOD_TYPE.NEGATIVE_LOG) {
                 mult = -1.0;
             }
             // one of us in log, the other negitive log, it doesn't matter which
@@ -265,7 +265,7 @@ public class LikelihoodObject {
             }
         } else if (likelihood == LIKELIHOOD_TYPE.RAW) {
             double mult = 1.0;
-            if (mLikelihoodType == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
+            if (mLikelihoodType == LIKELIHOOD_TYPE.NEGATIVE_LOG) {
                 mult = -1.0;
             }
             // one of us in log, the other negitive log, it doesn't matter which
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java
index 964dc9521..dc3a41925 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 /**
  * @author aaron
@@ -12,7 +12,21 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 public interface VariantBackedByGenotype {
     /**
      * get the likelihoods
+     *
+     * @param x the genotype
+     *
      * @return an array in lexigraphical order of the likelihoods
      */
     public Genotype getGenotype(DiploidGenotype x);
+
+
+    /**
+     * do we have the specified genotype?  not all backedByGenotypes
+     * have all the genotype data.
+     *
+     * @param x the genotype
+     *
+     * @return true if available, false otherwise
+     */
+    public boolean hasGenotype(DiploidGenotype x);
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Variation.java b/java/src/org/broadinstitute/sting/utils/genotype/Variation.java
index 5954f661a..fdc8feaec 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/Variation.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/Variation.java
@@ -58,7 +58,7 @@ public interface Variation {
      *
      * @return the reference base or bases, as a string
      */
-    public char getReference();
+    public String getReference();
 
     /**
      * get the -1 * (log 10 of the error value)
@@ -80,16 +80,22 @@ public interface Variation {
     public String getAlternateBases();
 
     /**
-     * are we an insertion or a deletion? yes, then return true.  No? Well, false it is.
+     * are we an insertion or a deletion? yes, then return true.  No? Well, false then.
      * @return true if we're an insertion or deletion
      */
     public boolean isIndel();
 
     /**
-     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
      * of 
      * @return a char, representing the alternate base
      */
     public char getAlternativeBaseForSNP();
 
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     * @return a char, representing the alternate base
+     */
+    public char getReferenceForSNP();
+
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
index 6a516d253..eb562fda0 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.genotype.geli;
 
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.*;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
index 893b54a27..4deee697b 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
@@ -6,7 +6,6 @@ import net.sf.samtools.util.BinaryCodec;
 import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.*;
 
 import java.io.DataOutputStream;
@@ -121,7 +120,7 @@ public class GLFWriter implements GenotypeWriter {
             Arrays.fill(values,-255.0);
             obj = new LikelihoodObject(values, LikelihoodObject.LIKELIHOOD_TYPE.LOG);
         }
-        obj.setLikelihoodType(LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);  // transform! ... to negitive log likelihoods
+        obj.setLikelihoodType(LikelihoodObject.LIKELIHOOD_TYPE.NEGATIVE_LOG);  // transform! ... to negitive log likelihoods
 
         double rms = -1;
         // calculate the RMS mapping qualities and the read depth
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java
index 886ab7747..96beac7b3 100644
--- a/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java
@@ -184,7 +184,7 @@ public class RodGLFTest extends BaseTest {
         for (int x = 0; x < vals.size(); x++) {
             ret[x] = vals.get(x);
         }
-        return new LikelihoodObject(ret, LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
+        return new LikelihoodObject(ret, LikelihoodObject.LIKELIHOOD_TYPE.NEGATIVE_LOG);
     }
 
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsTest.java
index 4131e5831..2f7207c22 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsTest.java
@@ -1,15 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.walkers.recalibration.RecalData;
-import org.junit.Before;
 import org.junit.Test;
 import org.junit.Assert;
 
 import static java.lang.Math.log10;
-import static java.lang.Math.pow;
 
 public class GenotypeLikelihoodsTest extends BaseTest {
     private final static double DELTA = 1e-8;
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeTest.java b/java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeTest.java
new file mode 100644
index 000000000..6297e6d5e
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeTest.java
@@ -0,0 +1,104 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import org.broadinstitute.sting.BaseTest;
+import org.junit.Assert;
+import org.junit.Test;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class DiploidGenotypeTest
+ *
+ * Testing the basic functionality of the diploid genotype class
+ */
+public class DiploidGenotypeTest extends BaseTest {
+
+    @Test
+    public void testCreateDiploidFromString() {
+        String genotype = "AA";
+        DiploidGenotype g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "AC";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "AG";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "AT";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "CC";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "CG";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "CT";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "GG";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "GT";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+
+        genotype = "TT";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(genotype.equals(g.toString()));
+    }
+
+    @Test
+    public void testIsHet() {
+        String genotype = "AG";
+        DiploidGenotype g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(g.isHet());
+
+        genotype = "AA";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(!g.isHet());
+    }
+
+     @Test
+    public void testIsHom() {
+        String genotype = "AA";
+        DiploidGenotype g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(g.isHom());
+
+        genotype = "AG";
+        g = DiploidGenotype.valueOf(genotype);
+        Assert.assertTrue(!g.isHom());
+    }
+
+    @Test
+      public void testCreateGenotype() {
+        char ref = 'A';
+        DiploidGenotype g = DiploidGenotype.createGenotype(ref);
+        Assert.assertTrue("AA".equals(g.toString()));
+
+        ref = 'a';
+        g = DiploidGenotype.createGenotype(ref);
+        Assert.assertTrue("AA".equals(g.toString()));
+
+        ref = 't';
+        g = DiploidGenotype.createGenotype(ref);
+        Assert.assertTrue("TT".equals(g.toString()));
+
+        ref = 'T';
+        g = DiploidGenotype.createGenotype(ref);
+        Assert.assertTrue("TT".equals(g.toString()));
+
+    }
+
+
+}
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectTest.java b/java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectTest.java
index 97ae2fcff..a05d32bf7 100755
--- a/java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectTest.java
@@ -61,7 +61,7 @@ public class LikelihoodObjectTest extends BaseTest {
         for (int x = 0; x < 10; x++) {
             ray[x] = ( x * 25 );
         }
-        mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
+        mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGATIVE_LOG);
         assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
 
         int index = 0;
@@ -77,7 +77,7 @@ public class LikelihoodObjectTest extends BaseTest {
         for (int x = 0; x < 10; x++) {
             ray[x] = ( x * 25.0 );
         }
-        mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
+        mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGATIVE_LOG);
         assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
 
         int index = 0;
@@ -104,7 +104,7 @@ public class LikelihoodObjectTest extends BaseTest {
             ray[x] = ( 240.0 );
         }
         ray [5] = 0;
-        mLO = new LikelihoodObject(ray, LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
+        mLO = new LikelihoodObject(ray, LikelihoodObject.LIKELIHOOD_TYPE.NEGATIVE_LOG);
         assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
         short smallest = (short)mLO.getBestLikelihood();
         assertTrue(smallest == 0);