From 7d58db626e28283d472fe29d71643ce739eceace Mon Sep 17 00:00:00 2001 From: Laurent Francioli Date: Wed, 30 Nov 2011 10:09:20 +0100 Subject: [PATCH] Added MendelianViolationEvaluator integration test --- .../varianteval/VariantEvalIntegrationTest.java | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 403ecce78..13876ff83 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -291,6 +291,17 @@ public class VariantEvalIntegrationTest extends WalkerTest { executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); } + @Test + public void testVEMendelianViolationEvaluator() { + String vcfFile = "/MendelianViolationEval.vcf"; + String pedFile = "/MendelianViolationEval.ped"; + + WalkerTestSpec spec = new WalkerTestSpec("-T VariantEval -R "+b37KGReference+" --eval " + variantEvalTestDataRoot + vcfFile + " -ped "+ variantEvalTestDataRoot + pedFile +" -noEV -EV MendelianViolationEvaluator -L 1:10109-10315 -o %s", + 1, + Arrays.asList("85a8fc01a1f50839667bfcd04155f735")); + executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec); + } + @Test public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";