From 0fa5a7af050b5c531c9281fc031fb926f3f1d5d2 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 15 Mar 2012 11:55:48 -0400
Subject: [PATCH] Adding contracts and unit tests for HaplotypeCaller
 GenotypingEngine

---
 .../utils/variantcontext/VariantContextUnitTest.java   | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
index 0e75eee14..318c2ce50 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -236,6 +236,16 @@ public class VariantContextUnitTest extends BaseTest {
         Assert.assertEquals(vc.getSampleNames().size(), 0);
     }
 
+    @Test
+    public void testMatchingAlleles() {
+        List<Allele> alleles = Arrays.asList(ATCref, del);
+        VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).referenceBaseForIndel((byte)'A').make();
+        VariantContext vc2 = new VariantContextBuilder("test2", delLoc, delLocStart+12, delLocStop+12, alleles).referenceBaseForIndel((byte)'A').make();
+
+        Assert.assertTrue(vc.hasSameAllelesAs(vc2));
+        Assert.assertTrue(vc.hasSameAlternateAllelesAs(vc2));
+    }
+
     @Test
     public void testCreatingInsertionVariantContext() {
         List<Allele> alleles = Arrays.asList(delRef, ATC);