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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
This commit is contained in:
ebanks 2011-04-29 16:03:45 +00:00
parent 96571b55be
commit ab9ffb1a74
1 changed files with 9 additions and 0 deletions
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9
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
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@ -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(