From b75a1807e3242fd3dda158aba33362f826fb9041 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 17 Aug 2011 22:40:09 -0400 Subject: [PATCH] Adding integration test to cover sample exclusion --- .../SelectVariantsIntegrationTest.java | 20 ++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index bec0d5dd4..cec377f5f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -7,7 +7,7 @@ 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; + return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s -NO_HEADER" + args; } @Test @@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile), 1, Arrays.asList("d18516c1963802e92cb9e425c0b75fd6") ); @@ -24,12 +24,26 @@ public class SelectVariantsIntegrationTest extends WalkerTest { executeTest("testComplexSelection--" + testfile, spec); } + @Test + public void testSampleExclusion() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant:VCF3 " + testfile, + 1, + Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd") + ); + + executeTest("testSampleExclusion--" + testfile, spec); + } + @Test public void testRepeatedLineSelection() { String testfile = validationDataLocation + "test.dup.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile), 1, Arrays.asList("b74038779fe6485dbb8734ae48178356") );