Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2531 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -29,7 +29,7 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal
     }
 
     public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
-        nSNPs += eval == null ? 0 : 1;
+        nSNPs += eval == null || eval.isReference()? 0 : 1;
 
         // TODO -- break the het check out to a different module used only for single samples
 

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

@@ -229,7 +229,12 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
     }
 
     public boolean hasAlternateAllele() {
-        return getAlternateAlleles().size() > 0;
+        for ( VCFGenotypeEncoding alt : this.mAlts ) {
+            if ( alt.getType() != VCFGenotypeEncoding.TYPE.UNCALLED )
+                return true;
+        }
+
+        return false;
     }
 
     public boolean isBiallelic() {
@@ -279,6 +284,9 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         switch ( type ) {
             case SINGLE_BASE:
                 return VARIANT_TYPE.SNP;
+            case UNCALLED:
+                // If there are no alt alleles, all of the genotypes are reference or no calls, so we're a reference site
+                return VARIANT_TYPE.REFERENCE;
             case DELETION:
                 return VARIANT_TYPE.DELETION;
             case INSERTION:

java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java

@@ -116,7 +116,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalGenotypeROD() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("978176e0b369c08c041a66045e995129");
+        md5.add("010d1c7ce773b39f3de1355eb9682e4d");
         /**
          * the above MD5 was calculated after running the following command:
          *