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Disabling parallelized version of VE integration tests. Still slow, but not 

deadlocking any more.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4580 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-10-27 02:47:03 +00:00
parent ffc0ed2b32
commit 04e38929f0
1 changed files with 16 additions and 8 deletions
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24
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -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) {