From 2586f0a1ca0bcbee372208ce77bf5fd2ef27be9c Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 21 Sep 2010 15:35:25 +0000 Subject: [PATCH] fix for the build I broke - the original file got corrupted, which I replaced with a version that didn't have the header stripped off. Other integration tests passed, but this test relied on the header being stripped off. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4320 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/variantutils/LiftoverVariantsIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 27e7a34c6..32dd48f8e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testb36Tohg19() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", + "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", 1, Arrays.asList("1637877892a019061e74eb3d9a9d100f")); executeTest("test b36 to hg19", spec);