-Renamed rodVariants to RodGeliText

-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java

@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.gatk.refdata.RodGeliText;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 import net.sf.samtools.SAMRecord;
@@ -36,11 +36,11 @@ public class VariantContext {
     private RefMetaDataTracker tracker;
     private ReferenceContext ref;
     private AlignmentContext context;
-    private rodVariants variant;
+    private RodGeliText variant;
     private AlignmentContext Q0freeContext = null;
 
     public VariantContext(RefMetaDataTracker tracker, ReferenceContext ref,
-                          AlignmentContext context, rodVariants variant) {
+                          AlignmentContext context, RodGeliText variant) {
         this.tracker = tracker;
         this.ref = ref;
         this.context = context;
@@ -49,7 +49,7 @@ public class VariantContext {
 
     public RefMetaDataTracker getTracker() { return tracker; }
     public ReferenceContext getReferenceContext() { return ref; }
-    public rodVariants getVariant() { return variant; }
+    public RodGeliText getVariant() { return variant; }
     public AlignmentContext getAlignmentContext(boolean useMQ0Reads) {
         return (useMQ0Reads ? context : getQ0freeContext());
     }

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

@@ -1,61 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import java.util.*;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
-/**
- * loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
- * 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 class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
-    public KGenomesSNPROD(final String name) {
-        super(name);
-    }
-
-    public GenomeLoc getLocation() {
-        loc = GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
-        return loc;
-    }
-    public String getRefBasesFWD() { return this.get("2"); }
-    public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
-    public String getAltBasesFWD() { return this.get("3"); }
-    public char getAltSnpFWD() throws IllegalStateException {
-        if ( getAltBasesFWD().charAt(0) != getRefSnpFWD() )
-            return getAltBasesFWD().charAt(0);
-        return getAltBasesFWD().charAt(1);
-    }
-    public boolean isReference()   { return getVariationConfidence() < 0.01; }
-    public boolean isSNP()         { return ! isReference(); }
-    public boolean isInsertion()   { return false; }
-    public boolean isDeletion()    { return false; }
-    public boolean isIndel()       { return false; }
-    public double getMAF()         { return Double.parseDouble(this.get("4")); }
-    public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); }
-    public boolean isGenotype()    { return false; }
-    public double getVariationConfidence() { return Double.parseDouble(this.get("8")); }
-    public double getConsensusConfidence() { return -1; }
-    public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
-    public int getPloidy() throws IllegalStateException { return 2; }
-    public boolean isBiallelic()   { return true; }
-
-    // SNPCallFromGenotypes interface
-    public int nIndividuals()      { return -1; }
-    public int nHomRefGenotypes()  { return -1; }
-    public int nHetGenotypes()     { return -1; }
-    public int nHomVarGenotypes()  { return -1; }
-    public List<Genotype> getGenotypes() { return null; }
-    public int length() { return 1; }
-
-    public String toString() {
-        StringBuffer sb = new StringBuffer();
-        sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
-        sb.append(getRefSnpFWD() + "\t" + getGenotype().get(0) + "\t");
-        sb.append(getMAF() + "\t0\t0\t0\t" + getVariationConfidence());
-        return sb.toString();
-    }
-}

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

@@ -62,23 +62,21 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
 
     static {
         // All known ROD types
-        addModule("GFF", rodGFF.class);
+        addModule("GFF", RodGenotypeChipAsGFF.class);
         addModule("dbSNP", rodDbSNP.class);
         addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
         addModule("SAMPileup", rodSAMPileup.class);
         addModule("GELI", rodGELI.class);
-        addModule("FLT", rodFLT.class);
         addModule("RefSeq", rodRefSeq.class);
         addModule("Table", TabularROD.class);
         addModule("PooledEM", PooledEMSNPROD.class);
-        addModule("1KGSNPs", KGenomesSNPROD.class);
         addModule("CleanedOutSNP", CleanedOutSNPROD.class);
         addModule("SangerSNP", SangerSNPROD.class);
         addModule("SimpleIndel", SimpleIndelROD.class);
         addModule("PointIndel", PointIndelROD.class);
         addModule("HapMapGenotype", HapMapGenotypeROD.class);
         addModule("Intervals", IntervalRod.class);
-        addModule("Variants", rodVariants.class);
+        addModule("Variants", RodGeliText.class);
         addModule("GLF", RodGLF.class);
     }
 
@@ -232,7 +230,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         for (ReferenceOrderedDatum rec : this) {
             System.out.println(rec.toString());
 
-            rodGFF gff = (rodGFF) rec;
+            RodGenotypeChipAsGFF gff = (RodGenotypeChipAsGFF) rec;
             String[] keys = {"LENGTH", "ALT", "FOBARBAR"};
             for (String key : keys) {
                 System.out.printf("  -> %s is (%s)%n", key, gff.containsAttribute(key) ? gff.getAttribute(key) : "none");

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

@@ -32,7 +32,7 @@ import java.io.IOException;
 import java.util.List;
 import java.util.Arrays;
 
-public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVariant {
+public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVariant {
     public enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
     public GenomeLoc loc;
     public char refBase = 'N';
@@ -43,7 +43,7 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
     public double lodBtnb;
     public double[] genotypeLikelihoods = new double[10];
     
-    public rodVariants(final String name) {
+    public RodGeliText(final String name) {
         super(name);
     }
 

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

@@ -16,7 +16,7 @@ import java.util.regex.Pattern;
  * Time: 10:47:14 AM
  * To change this template use File | Settings | File Templates.
  */
-public class rodGFF extends BasicReferenceOrderedDatum implements AllelicVariant {
+public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements AllelicVariant {
     private String contig, source, feature, strand, frame;
     private long start, stop;
     private double score;
@@ -27,7 +27,7 @@ public class rodGFF extends BasicReferenceOrderedDatum implements AllelicVariant
     // Constructors
     //
     // ----------------------------------------------------------------------
-    public rodGFF(final String name) {
+    public RodGenotypeChipAsGFF(final String name) {
         super(name);        
     }
 

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

@@ -1,66 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import java.util.*;
-
-import org.broadinstitute.sting.utils.*;
-
-/**
- * 1	469	C	S	51	52	0.00	44	1	C	0	M
- * 1	492	C	Y	130	51	0.00	46	1	C	0	T
- * 1	20786	G	K	5	6	0.00	46	1	T	38	G
- *
- */
-public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
-    public rodFLT(final String name) {
-        super(name);
-    }
-
-    public GenomeLoc getLocation() {
-        loc = GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
-        return loc;
-    }
-    public String getRefBasesFWD() { return this.get("2"); }
-    public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
-    public String getAltBasesFWD() { return new String(BaseUtils.iupacToBases(this.get("3").charAt(0))); }
-    public char getAltSnpFWD() throws IllegalStateException {
-        char[] bases = BaseUtils.iupacToBases(this.get("3").charAt(0));
-        if ( bases[0] != getRefSnpFWD() )
-            return bases[0];
-        else
-            return bases[1];
-    }
-
-    public String toString() {
-        StringBuffer sb = new StringBuffer();
-        sb.append(loc.getContig() + "\t" + loc.getStart() + "\t");
-        sb.append(getRefSnpFWD() + "\t-1\t-1\t" + getAltBasesFWD());
-        for (int i=0; i < 12; i++)
-            sb.append("\t0");
-        return sb.toString();
-    }
-
-    public boolean isReference()   { return false; }
-    public boolean isSNP()         { return true; }
-    public boolean isInsertion()   { return false; }
-    public boolean isDeletion()    { return false; }
-    public boolean isIndel()       { return false; }
-    public double getMAF()         { return 0.0; }
-    public double getHeterozygosity() { return 0.0; }
-    public boolean isGenotype()    { return false; }
-    public double getVariationConfidence() {
-        double value = Double.parseDouble(this.get("6"));
-        return (value > 0.0 ? value : 1.0);
-    }
-    public double getConsensusConfidence() { return -1; }
-    public List<String> getGenotype() throws IllegalStateException { return Arrays.asList(getAltBasesFWD()); }
-    public int getPloidy() throws IllegalStateException { return 2; }
-    public boolean isBiallelic()   { return true; }
-    public int length() { return 1; }
-
-    // SNPCallFromGenotypes interface
-    public int nIndividuals()      { return -1; }
-    public int nHomRefGenotypes()  { return -1; }
-    public int nHetGenotypes()     { return -1; }
-    public int nHomVarGenotypes()  { return -1; }
-    public List<Genotype> getGenotypes() { return null; }
-}

java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java

@@ -2,10 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.Utils;
@@ -85,7 +82,7 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
             }
             */
 
-            if ( datum != null && (datum instanceof rodGFF)) {
+            if ( datum != null && (datum instanceof RodGenotypeChipAsGFF)) {
                 rodString += "Hapmap: " + datum.toSimpleString() + " ";
             }
         }

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

@@ -1,10 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.gatk.contexts.VariantContext;
-import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.gatk.refdata.RodGeliText;
 import org.broadinstitute.sting.utils.*;
 import org.apache.log4j.Logger;
-import cern.jet.math.Arithmetic;
 
 
 public abstract class RatioFilter implements VariantExclusionCriterion {
@@ -37,14 +36,14 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         highThreshold = threshold;
     }
 
-    protected abstract Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, rodVariants variant);
+    protected abstract Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant);
     protected abstract boolean excludeHetsOnly();
 
     public boolean useZeroQualityReads() { return false; }
 
     public void compute(VariantContextWindow contextWindow) {
         VariantContext context = contextWindow.getContext();
-        rodVariants variant = context.getVariant();
+        RodGeliText variant = context.getVariant();
         char ref = context.getReferenceContext().getBase();
 
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads()));

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

@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.gatk.refdata.RodGeliText;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.Pair;
@@ -30,7 +30,7 @@ public class VECAlleleBalance extends RatioFilter {
      * Return the count of bases matching the major (first) and minor (second) alleles as a pair.
      *
      */
-    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, rodVariants variant) {
+    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype();
         final String bases = pileup.getBases();
 

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

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.VariantContext;
-import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.gatk.refdata.RodGeliText;
 import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.SAMRecord;
 import cern.jet.math.Arithmetic;
@@ -23,7 +23,7 @@ public class VECFisherStrand implements VariantExclusionCriterion {
 
     public void compute(VariantContextWindow contextWindow) {
         VariantContext context = contextWindow.getContext();
-        rodVariants variant = context.getVariant();
+        RodGeliText variant = context.getVariant();
         int allele1 = BaseUtils.simpleBaseToBaseIndex(variant.getBestGenotype().charAt(0));
         int allele2 = BaseUtils.simpleBaseToBaseIndex(variant.getBestGenotype().charAt(1));
 

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

@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.gatk.refdata.RodGeliText;
 import org.broadinstitute.sting.utils.*;
 
 public class VECOnOffGenotypeRatio extends RatioFilter {
@@ -26,7 +26,7 @@ public class VECOnOffGenotypeRatio extends RatioFilter {
      * best genotype).  On are in the first field, off in the second.
      *
     */
-    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, rodVariants variant) {
+    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype().toUpperCase();
         final String bases = pileup.getBases();
 

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

@@ -17,7 +17,7 @@ import java.util.*;
  * The former modifiesthe likelihoods of each genotype, while the latter makes a decision to include or exclude a
  * variant outright.  At the moment, the variants are expected to be in gelitext format.
  */
-@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=rodVariants.class))
+@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type= RodGeliText.class))
 public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
     @Argument(fullName="variants_out_head", shortName="VOH", doc="File to which modified variants should be written") public String VARIANTS_OUT_HEAD;
     @Argument(fullName="features", shortName="F", doc="Feature test (optionally with arguments) to apply to genotype posteriors.  Syntax: 'testname[:arguments]'", required=false) public String[] FEATURES;
@@ -176,7 +176,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
      * @return 1 if the locus was successfully processed, 0 if otherwise
      */
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        rodVariants variant = (rodVariants) tracker.lookup("variant", null);
+        RodGeliText variant = (RodGeliText) tracker.lookup("variant", null);
 
         // Ignore places where we don't have a variant or where the reference base is ambiguous.
         if ( variant == null || BaseUtils.simpleBaseToBaseIndex(ref.getBase()) == -1 )
@@ -204,7 +204,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
         VariantContext context = variantContextWindow.getContext();
         if ( context == null )
             return;
-        rodVariants variant = context.getVariant();
+        RodGeliText variant = context.getVariant();
 
         HashMap<String, Double> exclusionResults = new HashMap<String, Double>();
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCall.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.*;
@@ -129,7 +128,7 @@ public class SSGenotypeCall implements Genotype, ReadBacked, GenotypesBacked, Li
                 mCompareTo = DiploidGenotype.valueOf(Utils.dupString(this.getReference(),2));
             } else {
                 Integer sorted[] = Utils.SortPermutation(mGenotypeLikelihoods.getPosteriors());
-                mCompareTo = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 1]];
+                mCompareTo = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 2]];
             }
         }
         return mCompareTo;

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java

@@ -4,7 +4,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
+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;
@@ -52,7 +52,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
 
     public List<String> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
 
-        rodGFF hapmap_chip = (rodGFF)tracker.lookup("hapmap-chip", null);
+        RodGenotypeChipAsGFF hapmap_chip = (RodGenotypeChipAsGFF)tracker.lookup("hapmap-chip", null);
         String hc_genotype;
 
         if (hapmap_chip != null) {

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java

@@ -45,7 +45,7 @@ public class VCFHeader {
      *
      * @param metaData     the meta data associated with this header
      */
-    protected VCFHeader(Map<String, String> metaData) {
+    public VCFHeader(Map<String, String> metaData) {
         for (String key : metaData.keySet()) mMetaData.put(key, metaData.get(key));
         checkVCFVersion();
     }
@@ -56,7 +56,7 @@ public class VCFHeader {
      * @param metaData            the meta data associated with this header
      * @param genotypeSampleNames the genotype format field, and the sample names
      */
-    protected VCFHeader(Map<String, String> metaData, List<String> genotypeSampleNames) {
+    public VCFHeader(Map<String, String> metaData, List<String> genotypeSampleNames) {
         for (String key : metaData.keySet()) mMetaData.put(key, metaData.get(key));
         for (String col : genotypeSampleNames) {
             if (!col.equals("FORMAT"))

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SSGenotypeCallTest.java

@@ -0,0 +1,115 @@
+package org.broadinstitute.sting.gatk.walkers.genotyper;
+
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class SSGenotypeCallTest
+ *         <p/>
+ *         test the SS Genotype call class
+ */
+public class SSGenotypeCallTest extends BaseTest {
+
+    // we need a fake GenotypeLikelihoods class
+    public class GenotypeLikelihoodsImpl extends GenotypeLikelihoods {
+
+        /**
+         * Must be overridden by concrete subclasses
+         *
+         * @param observedBase
+         * @param chromBase
+         * @param read
+         * @param offset
+         *
+         * @return
+         */
+        @Override
+        protected double log10PofTrueBaseGivenMiscall(char observedBase, char chromBase, SAMRecord read, int offset) {
+            return 0;  //To change body of implemented methods use File | Settings | File Templates.
+        }
+
+        public GenotypeLikelihoodsImpl() {
+            this.posteriors = new double[10];
+            for (int x = 0; x < 10; x++) {
+                posteriors[x] = -(x);
+            }
+            this.likelihoods = new double[10];
+            for (int x = 0; x < 10; x++) {
+                likelihoods[x] = -(x);
+            }
+        }
+    }
+
+
+    // make a fake read pile-up
+    public Pair<ReadBackedPileup, GenomeLoc> makePileup() {
+        List<SAMRecord> reads = new ArrayList<SAMRecord>();
+        List<Integer> offset = new ArrayList<Integer>();
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10000);
+        for (int x = 0; x < 10; x++) {
+            reads.add(ArtificialSAMUtils.createArtificialRead(header, "test", 0, 1, 100));
+            offset.add(10 - x);
+        }
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc("chr1", 1, 10);
+        return new Pair(new ReadBackedPileup(loc, 'A', reads, offset), loc);
+    }
+
+
+    @Test
+    public void testBestVrsRefSame() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call = new SSGenotypeCall(true, myPair.second, 'A', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(0, call.getNegLog10PError(), 0.0000001);
+    }
+
+    @Test
+    public void testBestVrsRef2() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call2 = new SSGenotypeCall(true, myPair.second, 'T', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(9, call2.getNegLog10PError(), 0.0000001);
+    }
+
+    @Test
+    public void testBestVrsRef3() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call3 = new SSGenotypeCall(true, myPair.second, 'C', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(4, call3.getNegLog10PError(), 0.0000001);
+    }
+
+
+    @Test
+    public void testBestVrsNextSame() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call = new SSGenotypeCall(false, myPair.second, 'A', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(1, call.getNegLog10PError(), 0.0000001);
+    }
+
+    @Test
+    public void testBestVrsNext2() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call2 = new SSGenotypeCall(false, myPair.second, 'A', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(1, call2.getNegLog10PError(), 0.0000001);
+    }
+
+    @Test
+    public void testBestVrsNext3() {
+        Pair<ReadBackedPileup, GenomeLoc> myPair = makePileup();
+        SSGenotypeCall call3 = new SSGenotypeCall(false, myPair.second, 'C', new GenotypeLikelihoodsImpl(), myPair.first);
+        Assert.assertEquals(1, call3.getNegLog10PError(), 0.0000001);
+    }
+}