Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1724 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -28,7 +28,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes,
      * @return
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return getAltBasesFWD();
     }
 
@@ -38,7 +38,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes,
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> str = new ArrayList<String>();
         str.add(this.getAltBasesFWD());
         return str;

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

@@ -161,9 +161,9 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
     @Override
     public char getAlternativeBaseForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if (getAlternateBase().charAt(0) == this.getReference().charAt(0))
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
-            return getAlternateBase().charAt(1);
+            return getAlternateBases().charAt(1);
-        return getAlternateBase().charAt(0);
+        return getAlternateBases().charAt(0);
 
     }
 
@@ -175,9 +175,9 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
     @Override
     public char getReferenceForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if (getAlternateBase().charAt(0) == this.getReference().charAt(0))
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
-            return getAlternateBase().charAt(0);
+            return getAlternateBases().charAt(0);
-        return getAlternateBase().charAt(1);
+        return getAlternateBases().charAt(1);
 
     }
 
@@ -259,7 +259,7 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
      * @return a string, of ploidy
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return this.getBestGenotype(0).toString();
     }
 
@@ -269,9 +269,9 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> list = new ArrayList<String>();
-        list.add(this.getAlternateBase());
+        list.add(this.getAlternateBases());
         return list; 
     }
 

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

@@ -193,7 +193,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      * @return a string, of ploidy
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return this.bestGenotype;
     }
 
@@ -203,9 +203,9 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> list = new ArrayList<String>();
-        list.add(this.getAlternateBase());
+        list.add(this.getAlternateBases());
         return list; 
     }
 

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

@@ -187,7 +187,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
      * @return
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return this.feature;
     }
 
@@ -197,9 +197,9 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> list = new ArrayList<String>();
-        list.add(this.getAlternateBase());
+        list.add(this.getAlternateBases());
         return list; 
     }
 

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

@@ -171,7 +171,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     /** are we bi-allelic? */
     @Override
     public boolean isBiallelic() {
-        return (this.getAlternateBases().size() == 1);
+        return (this.getAlternateBaseList().size() == 1);
     }
 
     /**
@@ -201,8 +201,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
      * @return
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
-        if (!this.isBiallelic()) throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBases instead");
+        if (!this.isBiallelic()) throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBaseList instead");
         return this.mCurrentRecord.getAlternateAlleles().get(0);
     }
 
@@ -212,7 +212,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         return this.mCurrentRecord.getAlternateAlleles();
     }
 

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

@@ -73,7 +73,7 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
      * @return
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
        return "";
     }
 
@@ -83,7 +83,7 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         return Arrays.asList(new String[]{""});
     }
 
@@ -171,4 +171,4 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
         }
         return KGENOMES_FORMAT;
     }
- }
+}

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

@@ -174,7 +174,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
      * @return a string, of ploidy
      */
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return getAllelesFWDString();
     }
 
@@ -184,9 +184,9 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> list = new ArrayList<String>();
-        list.add(this.getAlternateBase());
+        list.add(this.getAlternateBases());
         return list;
     }
 
@@ -204,9 +204,9 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
     public char getAlternativeBaseForSNP() {
         return getAltSnpFWD(); /*
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        if (getAlternateBase().charAt(0) == this.getReference())
+        if (getAlternateBases().charAt(0) == this.getReference())
-            return getAlternateBase().charAt(1);
+            return getAlternateBases().charAt(1);
-        return getAlternateBase().charAt(0); */
+        return getAlternateBases().charAt(0); */
     }
 
     /**

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

@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.gatk.contexts.VariantContext;
-import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.refdata.CleanedOutSNPROD;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.HashMap;
 
@@ -23,7 +26,7 @@ public class VECIndelArtifact implements VariantExclusionCriterion {
             return;
         }
 
-        AllelicVariant indelCall = (AllelicVariant)tracker.lookup("indels", null);
+        Variation indelCall = (Variation)tracker.lookup("indels", null);
         if ( indelCall != null ) {
             exclude = true;
             source = "IndelCall";

java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java

@@ -1,11 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 @WalkerName("SNPClusters")
 @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)})
@@ -19,7 +22,7 @@ public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
     }
 
     public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        AllelicVariant snp = (AllelicVariant)tracker.lookup("snps", null);
+        Variation snp = (Variation)tracker.lookup("snps", null);
         return (snp != null && snp.isSNP()) ? context.getLocation() : null;
     }
 

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

@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenotypeUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import java.util.List;
+import org.broadinstitute.sting.gatk.refdata.VariationRod;
-import java.util.Collection;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
+import org.broadinstitute.sting.utils.genotype.Variation;
 
 /**
  * Created by IntelliJ IDEA.
@@ -17,38 +17,42 @@ import java.util.Collection;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.REFERENCE)
-@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="child",type= AllelicVariant.class), @RMD(name="parent1",type= AllelicVariant.class), @RMD(name="parent2",type= AllelicVariant.class)})
+@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="child",type= VariationRod.class), @RMD(name="parent1",type= VariationRod.class), @RMD(name="parent2",type= VariationRod.class)})
 //@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="dbsnp",type=AllelicVariant.class)})
 public class DeNovoSNPWalker extends RefWalker<String, Integer>{
 
     public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        AllelicVariant child = (AllelicVariant)tracker.lookup("child", null);
+        Variation child = (Variation)tracker.lookup("child", null);
-        AllelicVariant parent1 = (AllelicVariant)tracker.lookup("parent1", null);
+        Variation parent1 = (Variation)tracker.lookup("parent1", null);
-        AllelicVariant parent2 = (AllelicVariant)tracker.lookup("parent2", null);
+        Variation parent2 = (Variation)tracker.lookup("parent2", null);
-        AllelicVariant dbsnp = (AllelicVariant)tracker.lookup("dbSNP", null);
+        Variation dbsnp = (Variation)tracker.lookup("dbSNP", null);
         if (child != null && parent1 != null && parent2 != null) {
+            if (!(parent1 instanceof VariantBackedByGenotype) || !(parent2 instanceof VariantBackedByGenotype))
+                        throw new StingException("Both parents ROD tracks must be backed by genotype data. Ensure that your parent rod(s) contain genotyping information");
             if (child.isSNP() &&
-                child.getVariationConfidence() > 5 && // BTR > 5
+                child.getNegLog10PError() > 5 && // BTR > 5
                 parent1.isReference() &&
-                parent1.getConsensusConfidence() > 5 &&
+                ((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError() > 5 &&
                 parent2.isReference() && 
-                parent2.getConsensusConfidence() > 5
+                ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError() > 5
                 ) {
 
-                double sumConfidences = 0.5 * (0.5 * child.getVariationConfidence() + Math.min(parent1.getConsensusConfidence(), parent2.getConsensusConfidence()));
+                double sumConfidences = 0.5 * (0.5 * child.getNegLog10PError() +
+                        Math.min(((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError(),
+                                 ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError()));
 
                 out.format("%s\t", child.getLocation().getContig());
                 out.format("%s\t", child.getLocation().getStart());
                 out.format("%.4f\t", sumConfidences);
-                out.format("%.4f\t", child.getVariationConfidence());
+                out.format("%.4f\t", child.getNegLog10PError());
-                out.format("%.4f\t", parent1.getConsensusConfidence());
+                out.format("%.4f\t", ((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError());
-                out.format("%.4f\t", parent2.getConsensusConfidence());
+                out.format("%.4f\t", ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError());
                 out.format("%s\t", dbsnp != null);
 
                 out.format ("%s\t", child.toString());
                 out.format ("%s\t", parent1.toString());
-                out.format ("%s", parent2.toSimpleString());
+                out.format ("%s", parent2.toString());
                 if (dbsnp != null)
                     out.format ("\tDBSNP\t:%s", dbsnp.toString());
                 out.println();

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

@@ -58,18 +58,18 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
         int truthIndex, callIndex;
         if (chip == null)
             truthIndex = UNKNOWN;
-        else if (chip.getAlternateBase().equals(g.toString()))
+        else if (chip.getAlternateBases().equals(g.toString()))
             truthIndex = REF;
-        else if (chip.getAlternateBase().charAt(0) != chip.getAlternateBase().charAt(1))
+        else if (chip.getAlternateBases().charAt(0) != chip.getAlternateBases().charAt(1))
             truthIndex = VAR_HET;
         else
             truthIndex = VAR_HOM;
 
         if (eval == null)
             callIndex = NO_CALL;
-        else if (eval.getAlternateBase().equals(g.toString()))
+        else if (eval.getAlternateBases().equals(g.toString()))
             callIndex = REF;
-        else if (eval.getAlternateBase().charAt(0) != eval.getAlternateBase().charAt(1))
+        else if (eval.getAlternateBases().charAt(0) != eval.getAlternateBases().charAt(1))
             callIndex = VAR_HET;
         else
             callIndex = VAR_HOM;

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

@@ -38,10 +38,10 @@ public class IndelMetricsAnalysis extends BasicVariantAnalysis implements Genoty
             else
                 throw new RuntimeException("Variation is indel, but isn't insertion or deletion!");
 
-            if ( eval.getAlternateBase().length() < 100 ) {
+            if ( eval.getAlternateBases().length() < 100 ) {
-                sizes[eval.isDeletion() ? 0 : 1][eval.getAlternateBase().length()]++;
+                sizes[eval.isDeletion() ? 0 : 1][eval.getAlternateBases().length()]++;
-                if ( eval.getAlternateBase().length() > maxSize )
+                if ( eval.getAlternateBases().length() > maxSize )
-                    maxSize = eval.getAlternateBase().length();
+                    maxSize = eval.getAlternateBases().length();
             }
         }
 

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

@@ -183,7 +183,7 @@ class PooledConcordanceTable {
 
     public boolean pooledCallIsRef(Variation eval, char ref) {
         // code broken out for easy alteration when we start using pool-specific variations
-        return eval.getAlternateBase().equalsIgnoreCase((Utils.dupString(ref,2)));
+        return eval.getAlternateBases().equalsIgnoreCase((Utils.dupString(ref,2)));
     }
 
     public int calculateNumFrequencyIndeces(int poolSize) {
@@ -207,7 +207,7 @@ class PooledConcordanceTable {
         for ( Variation eval : evals ) {
             if ( mismatchingCalls(firstEval, eval, ref) ) {
                 // todo -- make this not a StingException but go to the log
-                throw new StingException("Tri-Allelic Position "+eval.getAlternateBase()+"/"+firstEval.getAlternateBase() + " Ref: "+ ref + " not supported");
+                throw new StingException("Tri-Allelic Position "+eval.getAlternateBases()+"/"+firstEval.getAlternateBases() + " Ref: "+ ref + " not supported");
             } else {
                 alternateFrequency += calledVariantFrequency(eval,ref);
             }
@@ -231,10 +231,10 @@ class PooledConcordanceTable {
 
     public boolean mismatchingCalls(Variation eval, Variation chip, char ref) {
         // eval and chip guaranteed to be non-null
-        char chipF = chip.getAlternateBase().charAt(0);
+        char chipF = chip.getAlternateBases().charAt(0);
-        char chipS = chip.getAlternateBase().charAt(1);
+        char chipS = chip.getAlternateBases().charAt(1);
-        char evalF = chip.getAlternateBase().charAt(0);
+        char evalF = chip.getAlternateBases().charAt(0);
-        char evalS = chip.getAlternateBase().charAt(1);
+        char evalS = chip.getAlternateBases().charAt(1);
         boolean mismatch;
         if (chipF == ref) {
             if ( chipS == ref ) {
@@ -259,7 +259,7 @@ class PooledConcordanceTable {
 
     public double calledVariantFrequency( Variation var, char ref ) {
         // code broken out for easy alteration when we start using pool-specific variations
-        String varStr = var.getAlternateBase();
+        String varStr = var.getAlternateBases();
         double freq;
         if ( varStr.charAt(0) != ref && varStr.charAt(1) != ref ) {
             freq = (double) 2;

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

@@ -92,7 +92,7 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
         if (eval != null) {
             char alt = (eval.isSNP()) ? eval.getAlternativeBaseForSNP() : eval.getReference().charAt(0);
             if (dbSNP != null && dbSNP.isSNP())
-                return !dbSNP.getAlternateBase().contains(String.valueOf(alt));
+                return !dbSNP.getAlternateBases().contains(String.valueOf(alt));
         }
         return false;
     }
@@ -125,7 +125,7 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
             if (dbsnp.isSNP() && eval.isSNP() && discordantP(dbsnp, eval)) {
                 return String.format("Discordant [DBSNP %s] [EVAL %s]", dbsnp, eval);
             } else if (dbsnp.isIndel() && eval.isSNP()) {
-                return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getAlternateBase(), eval);
+                return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getAlternateBases(), eval);
             } else {
                 return null;
             }

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

@@ -83,7 +83,7 @@ public class BasicVariation implements Variation {
     }
 
     @Override
-    public String getAlternateBase() {
+    public String getAlternateBases() {
         return mBases;
     }
 
@@ -93,9 +93,9 @@ public class BasicVariation implements Variation {
      * @return
      */
     @Override
-    public List<String> getAlternateBases() {
+    public List<String> getAlternateBaseList() {
         List<String> list = new ArrayList<String>();
-        list.add(this.getAlternateBase());
+        list.add(this.getAlternateBases());
         return list;
     }
 
@@ -151,9 +151,9 @@ public class BasicVariation implements Variation {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
 
         // we know that if we're a snp, the reference is a single base, so charAt(0) is safe
-        if (getAlternateBase().charAt(0) == this.getReference().charAt(0))
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
-            return getAlternateBase().charAt(1);
+            return getAlternateBases().charAt(1);
-        return getAlternateBase().charAt(0);
+        return getAlternateBases().charAt(0);
     }
 
     /**
@@ -166,9 +166,9 @@ public class BasicVariation implements Variation {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
 
         // we know that if we're a snp, the reference is a single base, so charAt(0) is safe
-        if (getAlternateBase().charAt(0) == this.getReference().charAt(0))
+        if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
-            return getAlternateBase().charAt(0);
+            return getAlternateBases().charAt(0);
-        return getAlternateBase().charAt(1);
+        return getAlternateBases().charAt(1);
     }
 
 

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

@@ -18,17 +18,21 @@ public interface Variation {
     }
 
     /**
-     * get the frequency of this variant
+     * get the frequency of this variant, if we're a variant.  If we're reference this method
+     * should return 0.
      *
-     * @return VariantFrequency with the stored frequency
+     * @return double with the stored frequency
      */
     public double getNonRefAlleleFrequency();
 
-    /** @return the VARIANT_TYPE of the current variant */
+    /**
+     * A convenience method, for switching over the variation type
+     * @return the VARIANT_TYPE of the current variant
+     **/
     public VARIANT_TYPE getType();
 
     /**
-     * are we a SNP? If not we're a Indel/deletion
+     * are we a SNP? If not we're a Indel/deletion or the reference
      *
      * @return true if we're a SNP
      */
@@ -42,12 +46,19 @@ public interface Variation {
     public boolean isInsertion();
 
     /**
-     * are we an insertion?
+     * are we an deletion?
      *
      * @return true if we are, false otherwise
      */
     public boolean isDeletion();
 
+    /**
+     * are we a variant that represents the reference allele?
+     *
+     * @return false if we're a variant(indel, delete, SNP, etc), true if we're hom ref
+     */
+    public boolean isReference();
+
     /**
      * get the location that this Variant represents
      *
@@ -68,33 +79,26 @@ public interface Variation {
     /**
      * get the -1 * (log 10 of the error value)
      *
-     * @return the log based error estimate
+     * @return the postive number space log based error estimate
      */
     public double getNegLog10PError();
 
-    /**
-     * are we truely a variant, given a reference
-     *
-     * @return false if we're a variant(indel, delete, SNP, etc), true if we're not
-     */
-    public boolean isReference();
-
     /**
      * gets the alternate base.  Use this method if we're biallelic
      *
      * @return
      */
-    public String getAlternateBase();
+    public String getAlternateBases();
 
     /**
-     * gets the alternate bases.  Use this method if teh allele count is greater then 2
+     * gets the alternate bases.  Use this method if the allele count is greater then 2 (not biallelic)
      *
      * @return
      */
-    public List<String> getAlternateBases();
+    public List<String> getAlternateBaseList();
 
     /**
-     * are we an insertion or a deletion? yes, then return true.  No? Well, false then.
+     * are we an insertion or a deletion? yes, then return true.  No? false.
      *
      * @return true if we're an insertion or deletion
      */