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VariantEval Integration Test parameterized for new novelty stratification

This commit is contained in:
Mark DePristo 2011-08-04 18:08:47 -04:00
parent 9be1ee59cc
commit 9308fbe3fb
1 changed files with 5 additions and 5 deletions
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10
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -236,7 +236,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("db95c8af8ba549d38ca6741a59fd6892"));
1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
executeTestParallel("testSelect1", spec);
}
@ -283,7 +283,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:dbsnp,VCF " + b37dbSNP132 +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("61c36fb6cc75172e2b22a44edeae85e0"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0897dfba2f4a245faddce38000555cce"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -295,7 +295,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("79895904a3c2799e2e384a933d10f3fc"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ead3602e14ec2944b5d9e4dacc08c819"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@ -312,13 +312,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9f906c04a4553d649b51ae67e0a25113"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("167a347ce0729d1bc3d4fd5069ebd674"));
executeTestParallel("testMultipleCompTracks",spec);
}
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
String md5 = "97a16a99a43d2384cfabc39d36647419";
String md5 = "40471a84b501eb440ee2d42e3081f228";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(