little fixes; also fixed a tyPo

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1662 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -352,7 +352,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      * @return a map in lexigraphical order of the genotypes
      */
     @Override
-    public Genotype getCallexGenotype() {
+    public Genotype getCalledGenotype() {
         return new BasicGenotype(getLocation(), this.getAltBasesFWD(), refBase, lodBtnb);
     }
 

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

@@ -265,7 +265,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
      * @return a map in lexigraphical order of the genotypes
      */
     @Override
-    public Genotype getCallexGenotype() {
+    public Genotype getCalledGenotype() {
         return new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence());
     }
 

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

@@ -255,7 +255,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
      * @return a map in lexigraphical order of the genotypes
      */
     @Override
-    public Genotype getCallexGenotype() {
+    public Genotype getCalledGenotype() {
         throw new UnsupportedOperationException("We don't support this right now"); 
     }
 
@@ -283,6 +283,27 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
         return genotypes;
     }
 
+    /**
+     * a private helper method
+     *
+     * @return an array in lexigraphical order of the likelihoods
+     */
+    private Genotype getGenotype(DiploidGenotype x) {
+        if (x.toString().equals(getReference()))
+            return new BasicGenotype(this.getLocation(), getReference(), this.getReference().charAt(0), 0);
+        for (VCFGenotypeRecord record : mCurrentRecord.getVCFGenotypeRecords()) {
+            if (Utils.join("", record.getAlleles()).equals(x.toString())) {
+                double qual = 0.0;
+                if (record.getAlleles().equals(this.getReference()))
+                    qual = this.getNegLog10PError();
+                else if (record.getFields().containsKey("GQ"))
+                    qual = Double.valueOf(record.getFields().get("GQ")) / 10.0;
+                return new BasicGenotype(this.getLocation(), Utils.join("", record.getAlleles()), this.getReference().charAt(0), qual);
+            }
+        }
+        return null;
+    }
+
     /**
      * do we have the specified genotype?  not all backedByGenotypes
      * have all the genotype data.
@@ -293,7 +314,9 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
      */
     @Override
     public boolean hasGenotype(DiploidGenotype x) {
-        return (this.getAlternateBases().contains(x.toString()));
+        if (getGenotype(x) != null)
+            return true;
+        return false;
     }
 
     @Override

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

@@ -358,7 +358,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
      * @return a map in lexigraphical order of the genotypes
      */
     @Override
-    public org.broadinstitute.sting.utils.genotype.Genotype getCallexGenotype() {
+    public org.broadinstitute.sting.utils.genotype.Genotype getCalledGenotype() {
         return new BasicGenotype(this.getLocation(), this.getAltBasesFWD(), this.getRefSnpFWD(), this.getConsensusConfidence());
     }
 

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

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -69,7 +68,7 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
         // For every threshold, updated discoverable and callable
         for (int i = 0; i < thresholds.length; i++) {
             double threshold = thresholds[i];
-            Genotype genotype = ((VariantBackedByGenotype)eval).getGenotypes().get(0);
+            Genotype genotype = ((VariantBackedByGenotype)eval).getCalledGenotype();
 
             // update discoverable
             if ( eval.isSNP() && eval.getNegLog10PError() >= threshold)

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

@@ -15,7 +15,7 @@ public interface VariantBackedByGenotype {
      *
      * @return a specific genotype that represents the called genotype
      */
-    public Genotype getCallexGenotype();
+    public Genotype getCalledGenotype();
 
     /**
      * get the genotype