From 28d8c8fcbc5487cd1525118cc38d8a9dc6f26663 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Mon, 8 Aug 2011 21:07:13 -0400 Subject: [PATCH] Modified the SnpEff integration test to run on a much smaller interval. --- .../walkers/annotator/VariantAnnotatorIntegrationTest.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 5dc7299a9..173c57a15 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -129,10 +129,11 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testSnpEffAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( - "-T VariantAnnotator -R " + b37KGReference + " -o %s -A SnpEff -B:variant,VCF " + validationDataLocation + "/1000G.exomes.vcf " + - "-B:SnpEff,SnpEff " + validationDataLocation + "/snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out" + " -L 1", + "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff -B:variant,VCF " + + validationDataLocation + "1000G.exomes.vcf -B:SnpEff,SnpEff " + validationDataLocation + + "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000", 1, - Arrays.asList("5fe3644744d3c084a179c3d204555333") + Arrays.asList("c08648a078368c80530bff004b3157f1") ); executeTest("Testing SnpEff annotations", spec); }