Changes to switch Variant Eval over to the new Variation system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
+import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.glf.GLFReader;
 import org.broadinstitute.sting.utils.genotype.glf.GLFRecord;
 import org.broadinstitute.sting.utils.genotype.glf.SinglePointCall;
@@ -13,9 +14,7 @@ import org.broadinstitute.sting.utils.genotype.glf.VariableLengthCall;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
 
 /**
@@ -25,7 +24,7 @@ import java.util.List;
  *         <p/>
  *         the rod class for GLF data.
  */
-public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<RodGLF> {
+public class RodGLF implements ReferenceOrderedDatum, Variation, Iterator<RodGLF> {
     static int count = 0;
     public GLFReader mReader;
     private final String mName;
@@ -38,6 +37,7 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
 
     /**
      * get the name
+     *
      * @return the name
      */
     @Override
@@ -64,27 +64,25 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         return toString();
     }
 
-    /**
+    /** @return a string representation of the ROD GLF object */
-     * @return a string representation of the ROD GLF object
-     */
     public String toString() {
         return String.format("%s\t%d\t%s\t%d\t%d\t%4.4f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f",
-                mLoc.getContig(),
+                             mLoc.getContig(),
-                mLoc.getStart(),
+                             mLoc.getStart(),
-                mRecord.getRefBase(),
+                             mRecord.getRefBase(),
-                mRecord.getReadDepth(),
+                             mRecord.getReadDepth(),
-                mRecord.getRmsMapQ(),
+                             mRecord.getRmsMapQ(),
-                getBestGenotypeValue(1),
+                             getBestGenotypeValue(1),
-                ((SinglePointCall)mRecord).getLikelihoods()[0],
+                             ((SinglePointCall) mRecord).getLikelihoods()[0],
-                ((SinglePointCall)mRecord).getLikelihoods()[1],
+                             ((SinglePointCall) mRecord).getLikelihoods()[1],
-                ((SinglePointCall)mRecord).getLikelihoods()[2],
+                             ((SinglePointCall) mRecord).getLikelihoods()[2],
-                ((SinglePointCall)mRecord).getLikelihoods()[3],
+                             ((SinglePointCall) mRecord).getLikelihoods()[3],
-                ((SinglePointCall)mRecord).getLikelihoods()[4],
+                             ((SinglePointCall) mRecord).getLikelihoods()[4],
-                ((SinglePointCall)mRecord).getLikelihoods()[5],
+                             ((SinglePointCall) mRecord).getLikelihoods()[5],
-                ((SinglePointCall)mRecord).getLikelihoods()[6],
+                             ((SinglePointCall) mRecord).getLikelihoods()[6],
-                ((SinglePointCall)mRecord).getLikelihoods()[7],
+                             ((SinglePointCall) mRecord).getLikelihoods()[7],
-                ((SinglePointCall)mRecord).getLikelihoods()[8],
+                             ((SinglePointCall) mRecord).getLikelihoods()[8],
-                ((SinglePointCall)mRecord).getLikelihoods()[9]
+                             ((SinglePointCall) mRecord).getLikelihoods()[9]
 
 
         );
@@ -107,6 +105,7 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
 
     /**
      * return a genome loc representing the current location
+     *
      * @return the geonome loc
      */
     @Override
@@ -115,62 +114,15 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
     }
 
     /**
-     * Returns bases in the reference allele as a String. String can be empty (as in insertion into
+     * get the reference base(s) at this position
-     * the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
-     * (for longer indels).
      *
-     * @return reference allele, forward strand
+     * @return the reference base or bases, as a string
      */
     @Override
-    public String getRefBasesFWD() {
+    public char getReference() {
-        if (mRecord.getRecordType() == GLFRecord.RECORD_TYPE.VARIABLE) return "";
-        return String.valueOf(mRecord.getRefBase());
-    }
-
-    /**
-     * Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
-     * if variant is not a SNP.
-     *
-     * This doesn't make much sense to me, what if the best genotype is hom non-ref?
-     *
-     * @return reference base on the forward strand
-     */
-    @Override
-    public char getRefSnpFWD() throws IllegalStateException {
-        if (!isSNP()) throw new IllegalStateException("Current GLF Record is not a SNP");
         return mRecord.getRefBase().toChar();
     }
 
-    /**
-     * 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
-     */
-    @Override
-    public String getAltBasesFWD() {
-        return getBestGenotype(2).toString();
-    }
-
-    /**
-     * 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
-     */
-    @Override
-    public char getAltSnpFWD() throws IllegalStateException {
-        if (!isSNP()) {
-            throw new IllegalStateException("Not a SNP");
-        }
-        String str = getBestGenotype(1).toString();
-        if (String.valueOf(str.charAt(0)).equals(mRecord.getRefBase().toString())) {
-            return str.charAt(1);
-        }
-        return str.charAt(0);
-    }
-
     /**
      * Returns true if all observed alleles are reference alleles. All is<Variant> methods (where Variant=SNP,Insertion, etc) should
      * return false at such site to ensure consistency. This method is included for use with genotyping calls (isGenotype()==true), it makes
@@ -183,6 +135,31 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         return (!isSNP());
     }
 
+    /**
+     * are we an insertion or a deletion? yes, then return true.  No? Well, false it is.
+     *
+     * @return true if we're an insertion or deletion
+     */
+    @Override
+    public boolean isIndel() {
+        return (isDeletion() || isInsertion());
+    }
+
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if (getAlternateBases().charAt(0) == this.getReference())
+            return getAlternateBases().charAt(1);
+        return getAlternateBases().charAt(0);
+
+    }
+
     /**
      * Is this variant a SNP?
      *
@@ -196,7 +173,9 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
 
     /**
      * return a string representing the reference
+     *
      * @param ref the reference character
+     *
      * @return a string for the homozygous ref in a diploid
      */
     private static String refString(char ref) {
@@ -213,7 +192,7 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
      */
     public LikelihoodObject.GENOTYPE getBestGenotype(int nthBest) {
         Integer[] sorted = Utils.SortPermutation(((SinglePointCall) mRecord).getLikelihoods());
-        return LikelihoodObject.GENOTYPE.values()[sorted[nthBest-1]];
+        return LikelihoodObject.GENOTYPE.values()[sorted[nthBest - 1]];
     }
 
     /**
@@ -226,7 +205,7 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
      */
     public double getBestGenotypeValue(int nthBest) {
         Integer[] sorted = Utils.SortPermutation(((SinglePointCall) mRecord).getLikelihoods());
-        return (((SinglePointCall) mRecord).getLikelihoods())[sorted[nthBest-1]];
+        return (((SinglePointCall) mRecord).getLikelihoods())[sorted[nthBest - 1]];
     }
 
     /**
@@ -254,16 +233,13 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
     }
 
     /**
-     * Is this variant an insertion or a deletion? The contract requires
+     * get the base representation of this Variant
-     * this to be true if either isInsertion() or isDeletion() returns true. However,
-     * this method is currently allowed to return true even if neither of isInsertion()
-     * and isDeletion() does.
      *
-     * @return
+     * @return a string, of ploidy
      */
     @Override
-    public boolean isIndel() {
+    public String getAlternateBases() {
-        return (mRecord.getRecordType() == GLFRecord.RECORD_TYPE.VARIABLE);
+        return this.getBestGenotype(0).toString();
     }
 
     /**
@@ -272,31 +248,19 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
      * @return
      */
     @Override
-    public double getMAF() {
+    public double getNonRefAlleleFrequency() {
         return 0;
     }
 
-    /**
+    /** @return the VARIANT_TYPE of the current variant */
-     * Returns heterozygosity, a more accessible general feature of a variant.
-     *
-     * @return
-     */
     @Override
-    public double getHeterozygosity() {
+    public VARIANT_TYPE getType() {
-        return 0;
+        if (this.isSNP()) return VARIANT_TYPE.SNP;
+        else if (this.isInsertion()) return VARIANT_TYPE.INDEL;
+        else if (this.isDeletion()) return VARIANT_TYPE.DELETION;
+        else return VARIANT_TYPE.REFERENCE;
     }
 
-    /**
-     * Is this variant an actual genotype (such as individual call from sequencing, HapMap chip etc), or
-     * population allelic variant (call from pooled sequencing, dbSNP site etc). Only if variant is a genotype, there
-     * is a meaningful question of, e.g., whether it is a het, or homogeneous non-ref.
-     *
-     * @return true if this variant is an actual genotype.
-     */
-    @Override
-    public boolean isGenotype() {
-        return true;
-    }
 
     /**
      * Returns phred-mapped confidence in variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
@@ -304,66 +268,20 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
      * @return
      */
     @Override
-    public double getVariationConfidence() {
+    public double getNegLog10PError() {
         String ref = new String() + mRecord.getRefBase() + mRecord.getRefBase();
         int index = 0;
-        for (LikelihoodObject.GENOTYPE g: LikelihoodObject.GENOTYPE.values()) {
+        for (LikelihoodObject.GENOTYPE g : LikelihoodObject.GENOTYPE.values()) {
             if (g.toString().equals(ref)) break;
             index++;
         }
-        return Math.abs(getBestGenotypeValue(1) - ((SinglePointCall)mRecord).getLikelihoods()[index]) / GLFRecord.LIKELIHOOD_SCALE_FACTOR;
+        return Math.abs(getBestGenotypeValue(1) - ((SinglePointCall) mRecord).getLikelihoods()[index]) / GLFRecord.LIKELIHOOD_SCALE_FACTOR;
     }
 
-    /**
+    public int length() {
-     * Returns phred-mapped confidence in called genotype (e.g. MAQ's consensus confidence, or AlleleCaller's
+        return 1;
-     * best vs next-best.
-     *
-     * @return
-     */
-    @Override
-    public double getConsensusConfidence() {
-        return Math.abs(getBestGenotypeValue(1) - getBestGenotypeValue(2)) / GLFRecord.LIKELIHOOD_SCALE_FACTOR;
     }
 
-    /**
-     * Returns actual observed genotype. Allowed to return more than two alleles (@see #getPloidy()). If this variant
-     * is not a genotype, should throw an IllegalStateException.
-     *
-     * @return
-     */
-    @Override
-    public List<String> getGenotype() throws IllegalStateException {
-        List<String> ret = new ArrayList<String>();
-        ret.add(this.getBestGenotype(1).toString());
-        return ret;
-    }
-
-    /**
-     * Return actual number of observed alleles (chromosomes) in the genotype. If this variant is not a genotype,
-     * should throw IllegalStateException.
-     *
-     * @return
-     */
-    @Override
-    public int getPloidy() throws IllegalStateException {
-        return 2; // we're so haploid it hurts
-    }
-
-    /**
-     * 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
-     */
-    @Override
-    public boolean isBiallelic() {
-        return false;
-    }
-
-    public int length() { return 1; }
-
     @Override
     public int compareTo(ReferenceOrderedDatum that) {
         return this.mLoc.compareTo(that.getLocation());
@@ -371,8 +289,10 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
 
     /**
      * the parse line, which is not used by the GLF rod
+     *
      * @param header the header to pass in
-     * @param parts the string object
+     * @param parts  the string object
+     *
      * @return false, alwayss
      * @throws java.io.IOException
      */

java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java

@@ -25,14 +25,19 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
+import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.genotype.BasicGenotype;
+import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.IOException;
-import java.util.List;
 import java.util.Arrays;
+import java.util.List;
 
-public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVariant {
+public class RodGeliText extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, AllelicVariant {
     public enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
     public GenomeLoc loc;
     public char refBase = 'N';
@@ -96,6 +101,27 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
 
     public GenomeLoc getLocation() { return loc; }
 
+    /**
+     * get the reference base(s) at this position
+     *
+     * @return the reference base or bases, as a string
+     */
+    @Override
+    public char getReference() {
+        return this.refBase;
+    }
+
+
+    /**
+     * get the -1 * (log 10 of the error value)
+     *
+     * @return the log based error estimate
+     */
+    @Override
+    public double getNegLog10PError() {
+        return Math.abs(lodBtr);
+    }
+
     public String getRefBasesFWD() {
         return String.format("%c", getRefSnpFWD());
     }
@@ -118,8 +144,24 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
         return refBase == bestGenotype.charAt(0) && refBase == bestGenotype.charAt(1);
     }
 
+    /**
+     * get the frequency of this variant
+     *
+     * @return VariantFrequency with the stored frequency
+     */
+    @Override
+    public double getNonRefAlleleFrequency() {
+        return 1.0;
+    }
+
+    /** @return the VARIANT_TYPE of the current variant */
+    @Override
+    public VARIANT_TYPE getType() {
+        return VARIANT_TYPE.SNP;
+    }
+
     public boolean isSNP() {
-        return !isReference();
+        return (!bestGenotype.equals(Utils.dupString(this.getReference(),2)));
     }
 
     public boolean isInsertion() {
@@ -130,10 +172,35 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
         return false;
     }
 
+    /**
+     * get the base representation of this Variant
+     *
+     * @return a string, of ploidy
+     */
+    @Override
+    public String getAlternateBases() {
+        return this.bestGenotype;
+    }
+
     public boolean isIndel() {
         return false;
     }
 
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if(this.bestGenotype.toString().charAt(0) == this.getReference())
+            return this.bestGenotype.toString().charAt(1);
+        return this.bestGenotype.toString().charAt(0);
+
+    }
+
     public double getMAF() {
         return 0;
     }
@@ -253,4 +320,15 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
     */
+
+    /**
+     * get the likelihoods
+     *
+     * @return an array in lexigraphical order of the likelihoods
+     */
+    @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());
+    }
 }

java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java

@@ -3,7 +3,9 @@ package org.broadinstitute.sting.gatk.refdata;
 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.Genotype;
 import java.util.*;
 import java.util.regex.MatchResult;
 import java.util.regex.Pattern;
@@ -16,7 +18,7 @@ import java.util.regex.Pattern;
  * Time: 10:47:14 AM
  * To change this template use File | Settings | File Templates.
  */
-public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements AllelicVariant {
+public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements AllelicVariant, Variation, VariantBackedByGenotype {
     private String contig, source, feature, strand, frame;
     private long start, stop;
     private double score;
@@ -74,6 +76,26 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
         return GenomeLocParser.parseGenomeLoc(contig, start, stop);
     }
 
+    /**
+     * get the reference base(s) at this position
+     *
+     * @return the reference base or bases, as a string
+     */
+    @Override
+    public char getReference() {
+        return 'N';
+    }
+
+    /**
+     * get the -1 * (log 10 of the error value)
+     *
+     * @return the log based error estimate
+     */
+    @Override
+    public double getNegLog10PError() {
+        return 4; // 1/10000 error
+    }
+
     public String getAttribute(final String key) {
         return attributes.get(key);
     }
@@ -158,10 +180,49 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
     public String getAltBasesFWD() { return null; }
     public char getAltSnpFWD() throws IllegalStateException { return 0; }
     public boolean isReference() { return ! isSNP(); }
+
+    /**
+     * gets the alternate bases.  If this is homref, throws an UnsupportedOperationException
+     *
+     * @return
+     */
+    @Override
+    public String getAlternateBases() {
+        return this.feature;
+    }
+
+    /**
+     * get the frequency of this variant
+     *
+     * @return VariantFrequency with the stored frequency
+     */
+    @Override
+    public double getNonRefAlleleFrequency() {
+        return this.getMAF();
+    }
+
+    /** @return the VARIANT_TYPE of the current variant */
+    @Override
+    public VARIANT_TYPE getType() {
+        return VARIANT_TYPE.SNP;
+    }
+
     public boolean isSNP() { return false; }
     public boolean isInsertion() { return false; }
     public boolean isDeletion() { return false; }
     public boolean isIndel() { return false; }
+
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        return this.getAltSnpFWD();
+    }
+
     public double getMAF() { return 0; }
     public double getHeterozygosity() { return 0; }
     public boolean isGenotype() { return true; }
@@ -175,4 +236,15 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
     public int length() { return 1; }
+
+    /**
+     * get the likelihoods
+     *
+     * @return an array in lexigraphical order of the likelihoods
+     */
+    @Override
+    public Genotype getGenotype(DiploidGenotype x) {
+        if (!x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
+        return new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence());
+    }
 }

java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java

@@ -7,12 +7,15 @@ import java.util.List;
  * chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0
  * chr1:1104841 C N 0.000000 -69.937928 -69.937928 0.000000 0.000000 324.000000 162 0 0
  * chr1:1104842 A N 0.000000 -84.816002 -84.816002 0.000000 0.000000 324.000000 162 0 0
- *
  */
 public interface SNPCallFromGenotypes extends AllelicVariant {
     public int nIndividuals();
+
     public int nHomRefGenotypes();
+
     public int nHetGenotypes();
+
     public int nHomVarGenotypes();
+
     public List<Genotype> getGenotypes();
 }

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -1,10 +1,12 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import net.sf.picard.util.SequenceUtil;
-
-import java.util.*;
-
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.genotype.*;
+import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Example format:
@@ -16,7 +18,7 @@ import org.broadinstitute.sting.utils.*;
  * Time: 10:47:14 AM
  * To change this template use File | Settings | File Templates.
  */
-public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVariant {
+public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, AllelicVariant {
     public GenomeLoc loc;       // genome location of SNP
                                 // Reference sequence chromosome or scaffold
                                 // Start and stop positions in chrom
@@ -60,6 +62,26 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
     // ----------------------------------------------------------------------
     public GenomeLoc getLocation() { return loc; }
 
+    /**
+     * get the reference base(s) at this position
+     *
+     * @return the reference base or bases, as a string
+     */
+    @Override
+    public char getReference() {
+        return getRefSnpFWD();
+    }
+
+    /**
+     * get the -1 * (log 10 of the error value)
+     *
+     * @return the log based error estimate
+     */
+    @Override
+    public double getNegLog10PError() {
+        return 4; // -log10(0.0001)
+    }
+
     public boolean onFwdStrand() {
         return strand.equals("+");
     }
@@ -108,10 +130,24 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
     }
 
     public String getAllelesFWDString() {
-        return Utils.join("/", getAllelesFWD());
+        return Utils.join("", getAllelesFWD());
     }
 
-    // ----------------------------------------------------------------------
+    /**
+     * get the frequency of this variant
+     *
+     * @return VariantFrequency with the stored frequency
+     */
+    @Override
+    public double getNonRefAlleleFrequency() {
+        return 0;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    /** @return the VARIANT_TYPE of the current variant */
+    @Override
+    public VARIANT_TYPE getType() {
+        return VARIANT_TYPE.SNP;
+    }// ----------------------------------------------------------------------
     //
     // What kind of variant are we?
     //
@@ -119,7 +155,34 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
     public boolean isSNP()              { return varType.contains("single"); }
     public boolean isInsertion()        { return varType.contains("insertion"); }
     public boolean isDeletion()         { return varType.contains("deletion"); }
+
+    /**
+     * get the base representation of this Variant
+     *
+     * @return a string, of ploidy
+     */
+    @Override
+    public String getAlternateBases() {
+        return getAllelesFWDString();
+    }
+
     public boolean isIndel()            { return isInsertion() || isDeletion() || varType.contains("in-del"); }
+
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        return getAltSnpFWD(); /*
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if (getAlternateBases().charAt(0) == this.getReference())
+            return getAlternateBases().charAt(1);
+        return getAlternateBases().charAt(0); */
+    }
+
     public boolean isReference()        { return false; } // snp locations are never "reference", there's always a variant
 
     public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
@@ -244,4 +307,14 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
     public int length() { return (int)(loc.getStop() - loc.getStart() + 1); }
 
+    /**
+     * get the likelihoods
+     *
+     * @return an array in lexigraphical order of the likelihoods
+     */
+    @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.getAltBasesFWD(),this.getRefSnpFWD(),this.getConsensusConfidence());
+    }
 }

java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.gatk.contexts.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RodGeliText;
+import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 import org.broadinstitute.sting.utils.*;
 import org.apache.log4j.Logger;
 
@@ -50,7 +51,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
 
         boolean highGenotypeConfidence = variant.getConsensusConfidence() > minGenotypeConfidenceToTest;
-        boolean excludable = !excludeHetsOnly() || GenotypeUtils.isHet(variant);
+        boolean excludable = !excludeHetsOnly() || GenotypeUtils.isHet((AllelicVariant)variant);
         exclude = excludable && highGenotypeConfidence && pointEstimateExclude(counts);
         //
         // for printing only

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicVariantAnalysis.java

@@ -1,12 +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.utils.genotype.Variation;
 
 import java.io.PrintStream;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
@@ -65,5 +65,5 @@ public abstract class BasicVariantAnalysis implements VariantAnalysis {
 
     }
 
-    public abstract String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context);
+    public abstract String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context);
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java

@@ -1,27 +1,30 @@
 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.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.Utils;
 
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
  * SOFTWARE COPYRIGHT NOTICE AGREEMENT
  * This software and its documentation are copyright 2009 by the
  * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
+ * <p/>
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
  */
 public class CallableBasesAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis {
     long all_bases = 0;
     long all_calls = 0;
     //final static double[] Qthresholds = { 10, 20, 30, 40, 50, 100, 200, 500, 1000 };
-    final static double[] thresholds = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100 };
+    final static double[] thresholds = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100};
     long[] discoverable_bases = new long[thresholds.length];
     long[] genotypable_bases = new long[thresholds.length];
 
@@ -29,36 +32,54 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
         super("callable_bases");
     }
 
-    public long nSites()                    { return all_bases; }
+    public long nSites() {
-    public long nCalls()                    { return all_calls; }
+        return all_bases;
-    public long nDiscoverable(int index)    { return discoverable_bases[index]; }
+    }
-    public double percentDiscoverable(int index)     { return (100.0*nDiscoverable(index)) / nSites(); }
-    public long nGenotypable(int index)     { return genotypable_bases[index]; }
-    public double percentGenotypable(int index)     { return (100.0*nGenotypable(index)) / nSites(); }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public long nCalls() {
+        return all_calls;
+    }
+
+    public long nDiscoverable(int index) {
+        return discoverable_bases[index];
+    }
+
+    public double percentDiscoverable(int index) {
+        return (100.0 * nDiscoverable(index)) / nSites();
+    }
+
+    public long nGenotypable(int index) {
+        return genotypable_bases[index];
+    }
+
+    public double percentGenotypable(int index) {
+        return (100.0 * nGenotypable(index)) / nSites();
+    }
+
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         all_bases++;
 
-        if ( eval == null )                     // no data here!
+        if (eval == null)                     // no data here!
             return null;
 
         // we actually have a record here
-        if ( ! eval.isGenotype() ) {            // evaluation record isn't a genotype, die!
+        if (!(eval instanceof VariantBackedByGenotype)) {            // evaluation record isn't a genotype, die!
             throw new RuntimeException("Evaluation track isn't an Genotype!");
         }
 
         all_calls++;
         // For every threshold, updated discoverable and callable
-        for ( int i = 0; i < thresholds.length; i++ ) {
+        for (int i = 0; i < thresholds.length; i++) {
             double threshold = thresholds[i];
-
+            DiploidGenotype g = DiploidGenotype.valueOf(Utils.dupString(ref, 2));
+            Genotype genotype = ((VariantBackedByGenotype) eval).getGenotype(g);
             // update discoverable
-            if ( eval.isSNP() && eval.getVariationConfidence() >= threshold )
+            if (eval.isSNP() && eval.getNegLog10PError() >= threshold)
                 discoverable_bases[i]++;
-            if ( eval.isReference() && eval.getConsensusConfidence() >= threshold )
+            if (!eval.isSNP() && genotype.getNegLog10PError() >= threshold)
                 discoverable_bases[i]++;
 
-            if ( eval.getConsensusConfidence() >= threshold )
+            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",
@@ -76,7 +97,7 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
         s.add(String.format(""));
         s.add(String.format("confidence_threshold\tdiscoverable_bases\tdiscoverable_bases_percent\tgenotypable_bases\tgenotypable_bases_percent"));
 
-        for ( int i = 0; i < thresholds.length; i++ ) {
+        for (int i = 0; i < thresholds.length; i++) {
             double threshold = thresholds[i];
             s.add(String.format("%6.2f\t%d\t%.6f\t%d\t%.6f", threshold, nDiscoverable(i), percentDiscoverable(i), nGenotypable(i), percentGenotypable(i)));
         }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ClusterCounterAnalysis.java

@@ -1,14 +1,14 @@
 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.refdata.IntervalRod;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.IntervalRod;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.ArrayList;
-import java.util.List;
 import java.util.HashSet;
+import java.util.List;
 
 /**
  * The Broad Institute
@@ -24,7 +24,7 @@ public class ClusterCounterAnalysis extends BasicVariantAnalysis implements Geno
     ArrayList<HashSet<GenomeLoc>> variantsWithClusters;
     int minDistanceForFlagging = 5;
     int[] neighborWiseBoundries = {1, 2, 5, 10, 20, 50, 100};
-    AllelicVariant lastVariant = null;
+    Variation lastVariation = null;
     GenomeLoc lastVariantInterval = null;
     int nSeen = 0;
 
@@ -36,16 +36,16 @@ public class ClusterCounterAnalysis extends BasicVariantAnalysis implements Geno
             variantsWithClusters.add(new HashSet<GenomeLoc>());
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         String r = null;
 
         if ( eval != null && eval.isSNP() ) {
             IntervalRod intervalROD = (IntervalRod)tracker.lookup("interval", null);
             GenomeLoc interval = intervalROD == null ? null : intervalROD.getLocation();
 
-            if (lastVariant != null) {
+            if (lastVariation != null) {
                 GenomeLoc eL = eval.getLocation();
-                GenomeLoc lvL = lastVariant.getLocation();
+                GenomeLoc lvL = lastVariation.getLocation();
                 if (eL.getContigIndex() == lvL.getContigIndex()) {
                     long d = eL.distance(lvL);
                     if ( lastVariantInterval != null && lastVariantInterval.compareTo(interval) != 0) {
@@ -66,7 +66,7 @@ public class ClusterCounterAnalysis extends BasicVariantAnalysis implements Geno
                 }
             }
 
-            lastVariant = eval;
+            lastVariation = eval;
             lastVariantInterval = interval;
         }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -1,21 +1,24 @@
 package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
-import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.*;
+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.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
  * SOFTWARE COPYRIGHT NOTICE AGREEMENT
  * This software and its documentation are copyright 2009 by the
  * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
+ * <p/>
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
  */
 public class GenotypeConcordance extends BasicVariantAnalysis implements GenotypeAnalysis {
     private String dbName;
@@ -35,48 +38,48 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
     public GenotypeConcordance(final String name) {
         super("genotype_concordance");
         dbName = name;
-        for ( int i = 0; i < 4; i++ ) {
+        for (int i = 0; i < 4; i++) {
             truth_totals[i] = 0;
             calls_totals[i] = 0;
-            for ( int j = 0; j < 4; j++ )
+            for (int j = 0; j < 4; j++)
                 table[i][j] = 0;
         }
     }
 
-    public void inc(AllelicVariant chip, AllelicVariant eval, char ref) {
+    public void inc(Variation chip, Variation eval, char ref) {
-        if ( (chip != null && !chip.isGenotype()) || (eval != null && !eval.isGenotype()) )
+        if ((chip != null && !(chip instanceof VariantBackedByGenotype) || (eval != null && !(eval instanceof VariantBackedByGenotype))))
             throw new StingException("Failure: trying to analyze genotypes of non-genotype data");
 
+        DiploidGenotype g = DiploidGenotype.valueOf(Utils.dupString(ref, 2));
         int truthIndex, callIndex;
-        if ( chip == null )
+        if (chip == null)
             truthIndex = UNKNOWN;
-        else if ( chip.isReference() && Utils.countOccurrences(ref, chip.getGenotype().get(0)) == chip.getGenotype().get(0).length() )
+        else if (chip.getAlternateBases().equals(g.toString()))
             truthIndex = REF;
-        else if ( GenotypeUtils.isHet(chip) )
+        else if (chip.getAlternateBases().charAt(0) != chip.getAlternateBases().charAt(1)) 
             truthIndex = VAR_HET;
         else
             truthIndex = VAR_HOM;
 
-        // todo -- FIXME on countOccurences
+        if (eval == null)
-        if ( eval == null )
             callIndex = NO_CALL;
-        else if ( eval.isReference() && Utils.countOccurrences(ref, eval.getGenotype().get(0)) == eval.getGenotype().get(0).length() )
+        else if (eval.getAlternateBases().equals(g.toString()))
             callIndex = REF;
-        else if ( GenotypeUtils.isHet(eval) )
+        else if (eval.getAlternateBases().charAt(0) != eval.getAlternateBases().charAt(1))
             callIndex = VAR_HET;
         else
             callIndex = VAR_HOM;
 
-        if ( chip != null || eval != null ) {
+        if (chip != null || eval != null) {
             //System.out.printf("TEST: %d/%d %s vs. %s%n", truthIndex, callIndex, chip, eval);
             table[truthIndex][callIndex]++;
             truth_totals[truthIndex]++;
-            if ( callIndex != NO_CALL ) calls_totals[callIndex]++;
+            if (callIndex != NO_CALL) calls_totals[callIndex]++;
         }
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
-        AllelicVariant chip = (AllelicVariant)tracker.lookup(dbName, null);
+        Variation chip = (Variation) tracker.lookup(dbName, null);
         inc(chip, eval, ref);
         return null;
     }
@@ -84,14 +87,14 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
     private void addCalledGenotypeConcordance(List<String> s) {
         StringBuilder sb = new StringBuilder();
         sb.append("CALLED_GENOTYPE_CONCORDANCE\t");
-        for ( int i = 0; i < 4; i++ ) {
+        for (int i = 0; i < 4; i++) {
             int nConcordantCallsI = table[i][i];
             String value = "N/A";
-            if ( i != UNKNOWN )
+            if (i != UNKNOWN)
-    	        value = String.format("%s\t", cellPercent(nConcordantCallsI, calls_totals[i]-table[UNKNOWN][i]));
+                value = String.format("%s\t", cellPercent(nConcordantCallsI, calls_totals[i] - table[UNKNOWN][i]));
             sb.append(value);
-    	}
+        }
-    	s.add(sb.toString());
+        s.add(sb.toString());
     }
 
     /**
@@ -99,9 +102,9 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
      */
     private int getNCalled() {
         int n = 0;
-        for ( int i = 0; i < 4; i++ )
+        for (int i = 0; i < 4; i++)
-            for ( int j = 0; j < 4; j++ )
+            for (int j = 0; j < 4; j++)
-                if ( i != NO_CALL && j != NO_CALL ) n += table[i][j];
+                if (i != NO_CALL && j != NO_CALL) n += table[i][j];
         return n;
     }
 
@@ -115,23 +118,23 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
         int nTrueVar = truth_totals[VAR_HET] + truth_totals[VAR_HOM];
         int nCalled = getNCalled();
         s.add(String.format("VARIANT_SENSITIVITY %s", cellPercent(nVarCalls, nTrueVar)));
-	    s.add(String.format("VARIANT_CONCORDANCE %s", cellPercent(nConcordantVarCalls, nVarCalls)));
+        s.add(String.format("VARIANT_CONCORDANCE %s", cellPercent(nConcordantVarCalls, nVarCalls)));
-	    s.add(String.format("OVERALL_CONCORDANCE %s", cellPercent(nConcordantCalls, nCalled)));
+        s.add(String.format("OVERALL_CONCORDANCE %s", cellPercent(nConcordantCalls, nCalled)));
     }
 
     public List<String> done() {
         List<String> s = new ArrayList<String>();
         s.add(String.format("name                 %s", dbName));
         s.add(String.format("TRUTH_STATE\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\tTOTALS\tTRUE_GENOTYPE_CONCORDANCE\tGENOTYPE_SENSITIVITY"));
-        for (int i=0; i < 4; i++) {
+        for (int i = 0; i < 4; i++) {
             StringBuffer sb = new StringBuffer();
             sb.append(String.format("%15s ", TRUTH_NAMES[i]));
-            for (int j=0; j < 4; j++)
+            for (int j = 0; j < 4; j++)
                 sb.append(String.format("%9d ", table[i][j]));
             sb.append(String.format("%9d ", truth_totals[i]));
-            if ( i == VAR_HET || i == VAR_HOM ) {
+            if (i == VAR_HET || i == VAR_HOM) {
-                sb.append(String.format("\t%s\t\t", cellPercent(table[i][i], table[i][REF]+table[i][VAR_HET]+table[i][VAR_HOM])));
+                sb.append(String.format("\t%s\t\t", cellPercent(table[i][i], table[i][REF] + table[i][VAR_HET] + table[i][VAR_HOM])));
-                sb.append(String.format("%s", cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i])));
+                sb.append(String.format("%s", cellPercent(truth_totals[i] - table[i][NO_CALL], truth_totals[i])));
             } else {
                 sb.append("\tN/A\t\t\tN/A");
             }
@@ -141,15 +144,15 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
         addCalledGenotypeConcordance(s);
         addOverallStats(s);
 
-        for (int i=0; i < 4; i++) {
+        for (int i = 0; i < 4; i++) {
-            for (int j=0; j < 4; j++) {
+            for (int j = 0; j < 4; j++) {
                 s.add(String.format("%s_%s_%s %d", TRUTH_NAMES[i], CALL_NAMES[j], "NO_SITES", table[i][j]));
                 s.add(String.format("%s_%s_%s %s", TRUTH_NAMES[i], CALL_NAMES[j], "PERCENT_OF_TRUTH", cellPercent(table[i][j], truth_totals[i])));
                 s.add(String.format("%s_%s_%s %s", TRUTH_NAMES[i], CALL_NAMES[j], "PERCENT_OF_CALLS", cellPercent(table[i][j], calls_totals[j])));
             }
-            if ( i == VAR_HET || i == VAR_HOM ) {
+            if (i == VAR_HET || i == VAR_HOM) {
-                s.add(String.format("%s_%s %s", TRUTH_NAMES[i], "TRUE_GENOTYPE_CONCORDANCE", cellPercent(table[i][i], table[i][REF]+table[i][VAR_HET]+table[i][VAR_HOM])));
+                s.add(String.format("%s_%s %s", TRUTH_NAMES[i], "TRUE_GENOTYPE_CONCORDANCE", cellPercent(table[i][i], table[i][REF] + table[i][VAR_HET] + table[i][VAR_HOM])));
-                s.add(String.format("%s_%s %s", TRUTH_NAMES[i], "GENOTYPE_SENSITIVITY", cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i])));
+                s.add(String.format("%s_%s %s", TRUTH_NAMES[i], "GENOTYPE_SENSITIVITY", cellPercent(truth_totals[i] - table[i][NO_CALL], truth_totals[i])));
             }
         }
         return s;
@@ -158,7 +161,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
     private static String cellPercent(int count, int total) {
         StringBuffer sb = new StringBuffer();
         total = Math.max(total, 0);
-        sb.append(String.format("%.2f", (100.0*count)/total));
+        sb.append(String.format("%.2f", (100.0 * count) / total));
         sb.append("%");
         return sb.toString();
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java

@@ -1,17 +1,16 @@
 package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
+import cern.jet.math.Arithmetic;
 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.refdata.SNPCallFromGenotypes;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import cern.jet.math.Arithmetic;
-
 /**
  * The Broad Institute
  * SOFTWARE COPYRIGHT NOTICE AGREEMENT
@@ -32,7 +31,7 @@ public class HardyWeinbergEquilibrium extends BasicVariantAnalysis implements Po
         this.threshold = threshold;
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         String r = null;
 
         if ( eval != null &&

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java

@@ -1,11 +1,11 @@
 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;
 
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
@@ -29,19 +29,19 @@ public class IndelMetricsAnalysis extends BasicVariantAnalysis implements Genoty
             sizes[0][i] = sizes[1][i] = 0;
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
-        if ( eval != null && eval.isIndel() ) {
+        if ( eval != null && eval.isInsertion() ) {
             if ( eval.isInsertion() )
                 insertions++;
             else if ( eval.isDeletion() )
                 deletions++;
             else
-                throw new RuntimeException("Variant is indel, but isn't insertion or deletion!");
+                throw new RuntimeException("Variation is indel, but isn't insertion or deletion!");
 
-            if ( eval.length() < 100 ) {
+            if ( eval.getAlternateBases().length() < 100 ) {
-                sizes[eval.isDeletion() ? 0 : 1][eval.length()]++;
+                sizes[eval.isDeletion() ? 0 : 1][eval.getAlternateBases().length()]++;
-                if ( eval.length() > maxSize )
+                if ( eval.getAlternateBases().length() > maxSize )
-                    maxSize = eval.length();
+                    maxSize = eval.getAlternateBases().length();
             }
         }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/NeighborDistanceAnalysis.java

@@ -1,15 +1,15 @@
 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.refdata.IntervalRod;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.IntervalRod;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
+import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.io.PrintStream;
 
 /**
  * The Broad Institute
@@ -26,7 +26,7 @@ public class NeighborDistanceAnalysis extends BasicVariantAnalysis implements Ge
     int minDistanceForFlagging = 5;
     int[] neighborWiseBoundries = {1, 2, 5, 10, 20, 50, 100, 1000, 10000};
 
-    AllelicVariant lastVariant = null;
+    Variation lastVariation = null;
     GenomeLoc lastVariantInterval = null;
     PrintStream violationsOut = null;
 
@@ -35,16 +35,16 @@ public class NeighborDistanceAnalysis extends BasicVariantAnalysis implements Ge
         neighborWiseDistances = new ArrayList<Long>();
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         String r = null;
 
         if ( eval != null && eval.isSNP() ) {
             IntervalRod intervalROD = (IntervalRod)tracker.lookup("interval", null);
             GenomeLoc interval = intervalROD == null ? null : intervalROD.getLocation();
 
-            if (lastVariant != null) {
+            if (lastVariation != null) {
                 GenomeLoc eL = eval.getLocation();
-                GenomeLoc lvL = lastVariant.getLocation();
+                GenomeLoc lvL = lastVariation.getLocation();
                 if (eL.getContigIndex() == lvL.getContigIndex()) {
                     long d = eL.distance(lvL);
                     if ( lastVariantInterval != null && lastVariantInterval.compareTo(interval) != 0) {
@@ -57,7 +57,7 @@ public class NeighborDistanceAnalysis extends BasicVariantAnalysis implements Ge
                 }
             }
             
-            lastVariant = eval;
+            lastVariation = eval;
             lastVariantInterval = interval;
         }
         

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java

@@ -1,9 +1,10 @@
 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.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -13,10 +14,9 @@ import java.util.List;
  * SOFTWARE COPYRIGHT NOTICE AGREEMENT
  * This software and its documentation are copyright 2009 by the
  * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
+ * <p/>
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
  */
 public class TransitionTranversionAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
     long nTransitions = 0, nTransversions = 0;
@@ -25,13 +25,18 @@ public class TransitionTranversionAnalysis extends BasicVariantAnalysis implemen
         super("transitions_transversions");
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
-        if ( eval != null && eval.isSNP() ) {
+        if (eval != null && eval.isSNP()) {
-            char refBase = eval.getRefSnpFWD();
+            if (eval.getAlternateBases().length() != 2) {
-            char altBase = eval.getAltSnpFWD();
+                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);
-            if ( subType == BaseUtils.BaseSubstitutionType.TRANSITION )
+            if (subType == BaseUtils.BaseSubstitutionType.TRANSITION)
                 nTransitions++;
             else
                 nTransversions++;

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantAnalysis.java

@@ -1,8 +1,8 @@
 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.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.PrintStream;
 import java.util.List;
@@ -23,7 +23,7 @@ public interface VariantAnalysis {
     public PrintStream getCallPrintStream();
     public List<String> getParams();
     public void initialize(VariantEvalWalker master, PrintStream out, PrintStream callOut, String filename);
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context);
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context);
     public void finalize(long nSites);
     public List<String> done();
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java

@@ -1,12 +1,13 @@
 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.AlignmentContext;
-import org.broadinstitute.sting.utils.GenotypeUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
@@ -27,10 +28,10 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal
         super("variant_counts");
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         nSNPs += eval == null ? 0 : 1;
 
-        if ( this.getMaster().evalContainsGenotypes && eval != null && eval.isSNP() && GenotypeUtils.isHet(eval) )
+        if ( this.getMaster().evalContainsGenotypes && eval != null && eval.isSNP() && ((VariantBackedByGenotype)eval).getGenotype( DiploidGenotype.valueOf(eval.getAlternateBases())).isHet() )
             nHets++;
 
         return null;

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java

@@ -1,21 +1,20 @@
 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.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The Broad Institute
  * SOFTWARE COPYRIGHT NOTICE AGREEMENT
  * This software and its documentation are copyright 2009 by the
  * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
+ * <p/>
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
  */
 public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
     private String dbName;
@@ -31,45 +30,81 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
         dbName = name;
     }
 
-    public void inc(AllelicVariant dbSNP, AllelicVariant eval) {
+    public void inc(Variation dbSNP, Variation eval) {
         boolean inDB = dbSNP != null;
         boolean inEval = eval != null;
 
-        if (inDB ) {
+        if (inDB) {
-            if ( dbSNP.isSNP() ) nDBSNPs++;
+            if (dbSNP.isSNP()) nDBSNPs++;
-            if ( dbSNP.isIndel() ) nDBIndels++;
+            if (dbSNP.isIndel()) nDBIndels++;
-
-            //System.out.printf("snp=%b ins=%b del=%b indel=%b %s%n", dbSNP.isSNP(), dbSNP.isInsertion(), dbSNP.isDeletion(), dbSNP.isIndel(), dbSNP);
         }
 
         if (inEval) nEvalObs++;
         if (inDB && inEval) {
-            if ( dbSNP.isSNP() ) { // changes the calculation a bit
+            if (dbSNP.isSNP()) { // changes the calculation a bit
                 nOverlapping++;
 
-                if ( ! discordantP(dbSNP, eval) )
+                if (!discordantP(dbSNP, eval))
                     nConcordant++;
             }
 
-            if ( dbSNP.isIndel() && eval.isSNP() )
+            if (dbSNP.isIndel() && eval.isSNP())
                 nSNPsCalledAtIndels++;
         }
     }
 
-    public int nDBSNPs()            { return nDBSNPs; }
+    public int callCount = 0;
-    public int nDBIndels()          { return nDBIndels; }
-    public int nEvalSites()         { return nEvalObs; }
-    public int nOverlappingSites()  { return nOverlapping; }
-    public int nConcordant()        { return nConcordant; }
-    public int nNovelSites()        { return Math.abs(nEvalSites() - nOverlappingSites()); }
-    public int nSNPsAtIndels()      { return nSNPsCalledAtIndels; }
 
-    public boolean discordantP(AllelicVariant dbSNP, AllelicVariant eval) {
+    public int nDBSNPs() {
-        if (dbSNP != null && dbSNP.isSNP() && eval != null ) {
+        return nDBSNPs;
-            return ! (dbSNP.getAltSnpFWD() == eval.getAltSnpFWD() || dbSNP.getRefSnpFWD() == eval.getAltSnpFWD());
+    }
-        } else {
+
-            return false;
+    public int nDBIndels() {
+        return nDBIndels;
+    }
+
+    public int nEvalSites() {
+        return nEvalObs;
+    }
+
+    public int nOverlappingSites() {
+        return nOverlapping;
+    }
+
+    public int nConcordant() {
+        return nConcordant;
+    }
+
+    public int nNovelSites() {
+        return Math.abs(nEvalSites() - nOverlappingSites());
+    }
+
+    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; 
+            }
         }
+        return false;
     }
 
 
@@ -86,17 +121,19 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
         return nConcordant() / (1.0 * nOverlappingSites());
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+
         // There are four cases here:
-        AllelicVariant dbsnp = (AllelicVariant)tracker.lookup(dbName, null);
+        Variation dbsnp = (Variation) tracker.lookup(dbName, null);
         boolean isSNP = dbsnp != null && dbsnp.isSNP();
         inc(dbsnp, eval);
 
-        if ( dbsnp != null && eval != null ) {
+        if (dbsnp != null && eval != null) {
-            if ( dbsnp.isSNP() && eval.isSNP() && discordantP(dbsnp, eval) ) {
+
+            if (dbsnp.isSNP() && eval.isSNP() && discordantP(dbsnp, eval)) {
                 return String.format("Discordant [DBSNP %s] [EVAL %s]", dbsnp, eval);
-            } else if ( dbsnp.isIndel() && eval.isSNP() ) {
+            } else if (dbsnp.isIndel() && eval.isSNP()) {
-                return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getGenotype().get(0), eval);
+                return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getAlternateBases(), eval);
             } else {
                 return null;
                 // return "Novel      " + eval;
@@ -128,10 +165,10 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
         s.add(String.format("n_concordant             %d", nConcordant()));
         s.add(String.format("n_novel_sites            %d", nNovelSites()));
 
-        s.add(String.format("percent_eval_sites_in_db %.2f", 100*fractionEvalSitesCoveredByDB()));
+        s.add(String.format("percent_eval_sites_in_db %.2f", 100 * fractionEvalSitesCoveredByDB()));
-        s.add(String.format("concordance_rate         %.2f", 100*concordanceRate()));
+        s.add(String.format("concordance_rate         %.2f", 100 * concordanceRate()));
 
-        s.add(String.format("percent_db_sites_in_eval %.2f", 100*fractionDBSitesDiscoveredInEval()));
+        s.add(String.format("percent_db_sites_in_eval %.2f", 100 * fractionDBSitesDiscoveredInEval()));
 
         s.add(String.format("n_snp_calls_at_indels    %d", nSNPsAtIndels()));
         s.add(String.format("percent_calls_at_indels  %.2f", nSNPsAtIndels() / (0.01 * nEvalSites())));

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -2,14 +2,12 @@ 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.AllelicVariant;
+import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.SNPCallFromGenotypes;
-import org.broadinstitute.sting.gatk.refdata.IntervalRod;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -28,8 +26,8 @@ import java.util.*;
  *
  */
 @By(DataSource.REFERENCE)
-@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=AllelicVariant.class)})
+@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=RodGeliText.class)}) // right now we have no base variant class for rods, this should change
-@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=AllelicVariant.class), @RMD(name="dbsnp",type=AllelicVariant.class),@RMD(name="hapmap-chip",type=AllelicVariant.class), @RMD(name="interval",type=IntervalRod.class)})
+@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=RodGeliText.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class)})
 public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
     public int minConfidenceScore = -1;
@@ -181,19 +179,18 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         nSites++;
-
         // Iterate over each analysis, and update it
-        AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null);
+        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.getConsensusConfidence() < minConfidenceScore ) eval = null;
+                if ( eval.getNegLog10PError() < minConfidenceScore ) eval = null;
             } else {
-                // Variant discovery - use best vs. reference lod
+                // Variation discovery - use best vs. reference lod
-                if ( Math.abs(eval.getVariationConfidence()) < minConfidenceScore ) eval = null;
+                if ( Math.abs(eval.getNegLog10PError()) < minConfidenceScore ) eval = null;
             }
         }
 
@@ -202,7 +199,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
 
         // update the known / novel set by checking whether the knownSNPDBName track has an entry here
         if ( eval != null ) {
-            AllelicVariant dbsnp = (AllelicVariant)tracker.lookup(knownSNPDBName, null);
+            Variation dbsnp = (Variation)tracker.lookup(knownSNPDBName, null);
             String noveltySet = dbsnp == null ? NOVEL_SNPS : KNOWN_SNPS;
             updateAnalysisSet(noveltySet, eval, tracker, ref.getBase(), context);
         }
@@ -219,7 +216,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     }
 
 
-    public void updateAnalysisSet(final String analysisSetName, AllelicVariant eval,
+    public void updateAnalysisSet(final String analysisSetName, Variation eval,
                                   RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         // Iterate over each analysis, and update it
         if ( getAnalysisSet(analysisSetName) != null ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java

@@ -1,8 +1,9 @@
 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.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 /**
  * The Broad Institute
@@ -22,7 +23,7 @@ public class VariantMatcher extends BasicVariantAnalysis implements GenotypeAnal
         dbName = name;
     }
 
-    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         String r = null;
         AllelicVariant db = (AllelicVariant)tracker.lookup(dbName, null);
         

java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java

@@ -0,0 +1,143 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class BasicGenotype
+ *
+ * represents a basic genotype object
+ */
+public class BasicGenotype implements Genotype {
+    // the genotype string
+    private String mGenotype;
+    private GenomeLoc mLocation;
+    private char mRef;
+    private double mNetLog10PError;
+
+    /**
+     * create a basic genotype
+     * @param genotype
+     */
+    public BasicGenotype(GenomeLoc location, String genotype, char ref, double netLog10PError) {
+        mNetLog10PError = netLog10PError;
+        mGenotype = genotype;
+        mLocation = location;
+        mRef = ref;
+    }
+
+    /**
+     * get the -1 * (log 10 of the error value)
+     *
+     * @return the log based error estimate
+     */
+    @Override
+    public double getNegLog10PError() {
+        return mNetLog10PError;
+    }
+
+    /**
+     * get the bases that represent this
+     *
+     * @return the bases, as a string
+     */
+    @Override
+    public String getBases() {
+        return mGenotype;
+    }
+
+    /**
+     * get the ploidy
+     *
+     * @return the ploidy value
+     */
+    @Override
+    public int getPloidy() {
+        return mGenotype.length();
+    }
+
+    /**
+     * Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
+     *
+     * @return true if we're homozygous, false otherwise
+     */
+    @Override
+    public boolean isHom() {
+        if (mGenotype.length() < 1)
+            return false;
+
+        char base = mGenotype.charAt(0);
+        for (char cur : mGenotype.toCharArray()) {
+            if (base != cur) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    /**
+     * Returns true if observed alleles differ (regardless of whether they are ref or alt)
+     *
+     * @return true if we're het, false otherwise
+     */
+    @Override
+    public boolean isHet() {
+        return !isHom();
+    }
+
+    /**
+     * get the genotype's location
+     *
+     * @return a GenomeLoc representing the location
+     */
+    @Override
+    public GenomeLoc getLocation() {
+        return mLocation;
+    }
+
+    /**
+     * returns true if the genotype is a point genotype, false if it's a indel / deletion
+     *
+     * @return true is a SNP
+     */
+    @Override
+    public boolean isPointGenotype() {
+        return true;
+    }
+
+    /**
+     * given the reference, are we a variant? (non-ref)
+     *
+     * @param ref the reference base or bases
+     *
+     * @return true if we're a variant
+     */
+    @Override
+    public boolean isVariant(char ref) {
+        return !(mGenotype.charAt(0) == ref && isHom());
+    }
+
+    /**
+     * get the reference base.
+     *
+     * @return a character, representing the reference base
+     */
+    @Override
+    public char getReference() {
+        return mRef;
+    }
+
+    /**
+     * return this genotype as a variant
+     *
+     * @return the variant
+     */
+    @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);
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java

@@ -8,7 +8,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
  * User: aaronmckenna
  * Date: Sep 9, 2009
  * Time: 9:32:34 PM
- *
+ * <p/>
  * a basic implementation of variant
  */
 public class BasicVariation implements Variation {
@@ -18,12 +18,14 @@ public class BasicVariation implements Variation {
     protected final int mLength;
     protected final GenomeLoc mLocation;
     protected final double mConfidence;
+
     /**
      * the constructor
-     * @param bases the bases that this variant represents
+     *
+     * @param bases     the bases that this variant represents
      * @param reference the reference base
-     * @param length are we a single base variant, or a indel/deletion? length is negitive for an indel,
+     * @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
+     *                  positive for a indel, and 0 for a substitution
      */
     public BasicVariation(String bases, char reference, int length, GenomeLoc location, double confidence) {
         mBases = bases;
@@ -40,14 +42,14 @@ public class BasicVariation implements Variation {
 
     @Override
     public VARIANT_TYPE getType() {
-        if (mLength >0) return VARIANT_TYPE.INDEL;
+        if (mLength > 0) return VARIANT_TYPE.INDEL;
-        if (mLength <0) return VARIANT_TYPE.DELETION;
+        if (mLength < 0) return VARIANT_TYPE.DELETION;
         return (isSNP()) ? VARIANT_TYPE.SNP : VARIANT_TYPE.REFERENCE;
     }
 
     @Override
     public boolean isSNP() {
-        if (mLength == 0 && Utils.dupString(mRef,2).equals(mBases)) return true;
+        if (mLength == 0 && Utils.dupString(mRef, 2).equals(mBases)) return true;
         return false;
     }
 
@@ -62,7 +64,7 @@ public class BasicVariation implements Variation {
     }
 
     @Override
-    public String getBases() {
+    public String getAlternateBases() {
         return mBases;
     }
 
@@ -72,19 +74,8 @@ public class BasicVariation implements Variation {
     }
 
     @Override
-    public String getReference() {
+    public char getReference() {
-        return String.valueOf(mRef);
+        return (mRef);
-    }
-
-    @Override
-    public boolean isHet() {
-        if (mLength == 0 && mBases.charAt(0) != mBases.charAt(1)) return true;
-        return false;
-    }
-
-    @Override
-    public boolean isHom() {
-        return !isHet();
     }
 
     @Override
@@ -98,12 +89,29 @@ public class BasicVariation implements Variation {
         return false;
     }
 
+    /**
+     * are we an insertion or a deletion? yes, then return true.  No? Well, false it is.
+     *
+     * @return true if we're an insertion or deletion
+     */
     @Override
-    public char getAlternateBase() {
+    public boolean isIndel() {
-        if (mLength != 0) {
+        return (isDeletion() || isInsertion());
-            throw new UnsupportedOperationException("Unable to get alternate base for indel / deletion");
-        }
-        if (mBases.charAt(0) == mRef) return mBases.charAt(1);
-        else return mBases.charAt(0);
     }
+
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException in the case
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
+        if (getAlternateBases().charAt(0) == this.getReference())
+            return getAlternateBases().charAt(1);
+        return getAlternateBases().charAt(0);
+    }
+
+
 }

java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java

@@ -0,0 +1,18 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Interface VariantBackedByGenotype
+ *         <p/>
+ *         this variant is backed by genotypic information
+ */
+public interface VariantBackedByGenotype {
+    /**
+     * get the likelihoods
+     * @return an array in lexigraphical order of the likelihoods
+     */
+    public Genotype getGenotype(DiploidGenotype x);
+}

java/src/org/broadinstitute/sting/utils/genotype/Variation.java

@@ -46,13 +46,6 @@ public interface Variation {
      */
     public boolean isDeletion();
 
-    /**
-     * get the base representation of this Variant
-     *
-     * @return a string, of ploidy
-     */
-    public String getBases();
-
     /**
      * get the location that this Variant represents
      *
@@ -65,13 +58,7 @@ public interface Variation {
      *
      * @return the reference base or bases, as a string
      */
-    public String getReference();
+    public char getReference();
-
-    /** is our base representation heterozygous */
-    public boolean isHet();
-
-    /** is our base representation homozygous */
-    public boolean isHom();
 
     /**
      * get the -1 * (log 10 of the error value)
@@ -87,9 +74,22 @@ public interface Variation {
     public boolean isReference();
 
     /**
-     * gets the alternate base.  If this is homref, throws an UnsupportedOperationException
+     * gets the alternate bases.  If this is homref, throws an UnsupportedOperationException
      * @return
      */
-    public char getAlternateBase();
+    public String getAlternateBases();
+
+    /**
+     * are we an insertion or a deletion? yes, then return true.  No? Well, false it is.
+     * @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
+     * of 
+     * @return a char, representing the alternate base
+     */
+    public char getAlternativeBaseForSNP();
 
 }

java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java

@@ -8,14 +8,12 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
 import org.junit.Assert;
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
@@ -60,38 +58,7 @@ public class RodGLFTest extends BaseTest {
         assertEquals(finalRecordCount, counter);
     }
 
-    /** make sure we're returning true to biallelic */
-    @Test
-    public void testIsBiallelic() {
-        RodGLF glf = iter.next();
-        Assert.assertFalse(iter.isBiallelic());
-    }
 
-    // best vs next-best
-    @Test
-    public void testGetConsensusConfidence() {
-        RodGLF glf = iter.next();
-        assertEquals(120.0, iter.getConsensusConfidence(), 0.005);
-        glf = iter.next();
-        assertEquals(120.0, iter.getConsensusConfidence(), 0.005);
-    }
-
-    // best vs. ref
-    @Test
-    public void testGetVariationConfidence() {
-        RodGLF glf = iter.next();
-        assertEquals(0.0, iter.getVariationConfidence(), 0.005);
-        glf = iter.next();
-        assertEquals(250.0, iter.getVariationConfidence(), 0.005);
-    }
-
-
-    @Test
-    public void testGetGenotype() {
-        RodGLF glf = iter.next();
-        List<String> str = iter.getGenotype();
-        Assert.assertTrue(str.get(0).equals("AA"));
-    }
 
     @Test
     public void testIsSNP() {
@@ -112,7 +79,7 @@ public class RodGLFTest extends BaseTest {
         glf = iter.next();
         Assert.assertFalse(iter.isReference());
     }
-
+    /*
     @Test(expected = IllegalStateException.class)
     public void testGetAltSnpFWDIllegalException() {
         RodGLF glf = iter.next();
@@ -159,7 +126,7 @@ public class RodGLFTest extends BaseTest {
     /**
      * move to the second and third bases, and check that the
      * alternate bases are correct.
-     */
+     *
     @Test
     public void testGetAltBasesFWD() {
         RodGLF glf = iter.next();
@@ -169,7 +136,7 @@ public class RodGLFTest extends BaseTest {
         Assert.assertTrue("CT".equals(iter.getAltBasesFWD()));
 
     }
-
+*/
     @Test
     public void testRodLocations() {
         GenomeLoc loc = null;
@@ -177,7 +144,7 @@ public class RodGLFTest extends BaseTest {
             RodGLF glf = iter.next();
             if (loc != null) {
                 if (iter.getLocation().isBefore(loc)) {
-                    fail("locations in the GLF came out of order loc = " + loc.toString() + " new loc = " + iter.getLocation().toString());
+                    Assert.fail("locations in the GLF came out of order loc = " + loc.toString() + " new loc = " + iter.getLocation().toString());
                 }
             }
             loc = iter.getLocation();

java/test/org/broadinstitute/sting/utils/genotype/BasicGenotypeTest.java

@@ -0,0 +1,62 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class BasicGenotypeTest
+ *
+ * tests the basic genotype class
+ */
+public class BasicGenotypeTest extends BaseTest {
+    private static IndexedFastaSequenceFile seq;
+
+       @BeforeClass
+       public static void beforeTests() {
+           try {
+               seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+           } catch (FileNotFoundException e) {
+               throw new StingException("unable to load the sequence dictionary");
+           }
+           GenomeLocParser.setupRefContigOrdering(seq);
+
+       }
+
+    @Test
+    public void testBasicGenotypeIsHom() {
+        BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA",'A',0);
+        Assert.assertTrue(gt.isHom());
+        BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA",'A',0);
+        Assert.assertTrue(!gt2.isHom());
+    }
+
+    @Test
+    public void testBasicGenotypeIsHet() {
+        BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA",'A',0);
+        Assert.assertTrue(!gt.isHet());
+        BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA",'A',0);
+        Assert.assertTrue(gt2.isHet());
+    }
+
+    @Test
+    public void testBasicGenotypeIsVariant() {
+        BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA",'A',0);
+        Assert.assertTrue(!gt.isVariant('A'));
+        BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA",'A',0);
+        Assert.assertTrue(gt2.isVariant('A'));
+        BasicGenotype gt3 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"TT",'A',0);
+        Assert.assertTrue(gt3.isVariant('A'));
+    }
+}