diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 929122885..3ba01f1d5 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -30,7 +30,8 @@ public class for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s", 1, Arrays.asList("158ac8e6d32eb2ea1bbeebfa512965de")); - executeTestParallel("testSelect1", spec); + //executeTestParallel("testSelect1", spec); + executeTest("testSelect1", spec); } } @@ -39,7 +40,8 @@ public class String extraArgs = "-L 1:1-10,000,000"; WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s", 1, Arrays.asList("cee96f61ffa1d042fe0c63550c508ec9")); - executeTestParallel("testSelect2", spec); + //executeTestParallel("testSelect2", spec); + executeTest("testSelect2", spec); } @Test @@ -49,7 +51,8 @@ public class WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s", 1, Arrays.asList("7e9ce1b26cdeaa50705f5de163847638")); - executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); + //executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); + executeTest("testVEGenotypeConcordance" + vcfFile, spec); } } @@ -67,7 +70,8 @@ public class WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s", 1, // just one output file Arrays.asList(md5)); - executeTestParallel("testVESimple", spec); + //executeTestParallel("testVESimple", spec); + executeTest("testVESimple", spec); } } } @@ -92,7 +96,8 @@ public class WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s", 1, // just one output file Arrays.asList(md5)); - executeTestParallel("testVEComplex", spec); + //executeTestParallel("testVEComplex", spec); + executeTest("testVEComplex", spec); } } } @@ -109,7 +114,8 @@ public class String md5 = "d41d8cd98f00b204e9800998ecf8427e"; WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5)); - executeTestParallel("testVEGenomicallyAnnotated", spec); + //executeTestParallel("testVEGenomicallyAnnotated", spec); + executeTest("testVEGenomicallyAnnotated", spec); } @Test @@ -119,7 +125,8 @@ public class WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER", 2, Arrays.asList("6b97a019402b3984fead9a4e8b7c7c2a", "989bc30dea6c8a4cf771cd1b9fdab488")); - executeTestParallel("testVEWriteVCF", spec); + //executeTestParallel("testVEWriteVCF", spec); + executeTest("testVEWriteVCF", spec); } } @@ -127,7 +134,8 @@ public class public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -E GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf -reportType CSV"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("25a681855cb26e7380fbf1a93de0a41f")); - executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec); + //executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec); + executeTest("testACDiscordanceAtAC1EvalAC2Comp",spec); } private static String withSelect(String cmd, String select, String name) {