From 13f29660bb518ed47d7660444ab5bb1196533965 Mon Sep 17 00:00:00 2001 From: kiran Date: Sun, 8 Aug 2010 05:49:47 +0000 Subject: [PATCH] Integration test for SelectVariants. Tests a complex case with an explicit sample selection, sample selection by regex, exclusion of non-variant and filtered loci, and JEXL selection on low allele-frequency variants git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3976 348d0f76-0448-11de-a6fe-93d51630548a --- .../SelectVariantsIntegrationTest.java | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java new file mode 100755 index 000000000..10fe44bfe --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -0,0 +1,25 @@ +package org.broadinstitute.sting.gatk.walkers.variantutils; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.Arrays; + +public class SelectVariantsIntegrationTest extends WalkerTest { + public static String baseTestString(String args) { + return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args; + } + + @Test + public void testComplexSelection() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -sn A -sn [CDEH] -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile), + 1, + Arrays.asList("3a15628b5980031c629c0c33e7e60b40") + ); + + executeTest("testComplexSelection--" + testfile, spec); + } +}