From 954dd84f518928bd78851fca1e516c4fa07e5f22 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 Oct 2010 07:45:21 +0000
Subject: [PATCH] Adding an integration test (against hg18 this time) that
 requires on-the-fly sorting in order to work properly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4500 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantutils/LiftoverVariantsIntegrationTest.java    | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index 32dd48f8e..785763dbd 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -43,4 +43,13 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
                  Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
          executeTest("test b36 to hg19", spec);
     }
+
+    @Test
+    public void testhg18Tohg19Unsorted() {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 "-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
+                 1,
+                 Arrays.asList("ce71a6d40f7375826e31adb3832d2fe3"));
+         executeTest("test hg18 to hg19, unsorted", spec);
+    }
 }
\ No newline at end of file