From 761a7307587dd7899e88fbb47721681278b5a474 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Oct 2009 00:09:46 +0000
Subject: [PATCH] assertBiAllelic -> assertMultiAllelic. Chris, if this breaks
 an integration test, you get it.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/refdata/RodVCF.java | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

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