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Update VE IT to reflect new fields and bugfixes

This commit is contained in:
Mark DePristo 2012-04-13 11:56:48 -04:00
parent f9190b6fcd
commit 3f6b2423d8
1 changed files with 6 additions and 6 deletions
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12
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -302,7 +302,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp: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("4c00cfa0fd343fef62d19af0edeb4f65"));
1, Arrays.asList("8d4530e9cef8531c46bbb693b84d04c7"));
executeTestParallel("testSelect1", spec);
}
@ -330,7 +330,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@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";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("4df6654860ad63b7e24e6bc5fbbbcb00"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("bb076f7239039191fde883c5e68483ea"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -360,7 +360,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --dbsnp " + b37dbSNP132 +
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3b85cd0fa37539ff51d34e026f26fef2"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9d24f34d94d74417e00e3b7bcf84650f"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -372,7 +372,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("bed8751c773b9568218f78c90f13348a"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("7329b0bc73c9ccaf5facd754f3410c38"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@ -488,7 +488,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("9726c0c8f19d271cf680f5f16f0926b3")
Arrays.asList("aad01b26198b30da5d59a05c08d863bb")
);
executeTest("testModernVCFWithLargeIndels", spec);
}
@ -508,7 +508,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("c89705147ef4233d5de3a539469bd1d1")
Arrays.asList("4fa2557663ef8fb4cdeecd667791985c")
);
executeTest("testStandardIndelEval", spec);
}