From c29924e7cfae515876abb73a2b3a1d27f7f91808 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Oct 2009 00:55:24 +0000
Subject: [PATCH] Reverting previous change. Aaron, it's all yours...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/refdata/RodVCF.java | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 1288cf6c9..172e30c52 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -77,9 +77,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return vcf;
     }
 
-    public void assertMultiAllelic() {
-        if (this.getAlternateBaseList().size() < 1)
-            throw new StingException("We're not multi-allelic.");
+    public void assertBiAllelic() {
+        if (!this.isBiallelic()) throw new StingException("We're not bi-allelic.");
     }
 
     /**
@@ -121,7 +120,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isSNP() {
         this.assertNotNull();
-        assertMultiAllelic();
+        assertBiAllelic();
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
             if (alt.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE)
                 return false;
@@ -137,7 +136,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isInsertion() {
         this.assertNotNull();
-        assertMultiAllelic();
+        assertBiAllelic();
         if (!mCurrentRecord.hasAlternateAllele())
             return false;
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
@@ -155,7 +154,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isDeletion() {
         this.assertNotNull();
-        assertMultiAllelic();
+        assertBiAllelic();
         if (!mCurrentRecord.hasAlternateAllele())
             return false;
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {