From ab9ffb1a7422d94469eaa89d0d81c6fe6759c126 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 29 Apr 2011 16:03:45 +0000 Subject: [PATCH] Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5711 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 005e7df2b..1dfdf5831 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -44,6 +44,15 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { executeTest("test b36 to hg19", spec); } + @Test + public void testb36Tohg19UnsortedSamples() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", + 1, + Arrays.asList("b6ef4a2f026fd3843aeb9ed764a66921")); + executeTest("test b36 to hg19, unsorted samples", spec); + } + @Test public void testhg18Tohg19Unsorted() { WalkerTestSpec spec = new WalkerTestSpec(