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Modified MD5s to account for Andrey's new MNP column in CountVariants. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5274 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-18 13:13:58 +00:00
parent cb95e68fc0
commit 52f860c9b2
1 changed files with 19 additions and 19 deletions
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38
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -56,7 +56,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("476b495de54e1a377c6895c02a6fdf6a")
Arrays.asList("e4545f524cc8386079dc9190de5d9bcc")
);
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
}
@ -89,7 +89,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("9f4e4fff339e725f42d65063e43e7d1c")
Arrays.asList("3dbefb800e432fdd237d6c57e4456352")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
}
@ -123,7 +123,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("369fa4f37bcc03b8a0bc1e58bf22bf0a")
Arrays.asList("9fafed19a700a7d4bd7aaed2dcad37be")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
}
@ -156,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("891ad0d38f1a1b08b31fe1cb6a3afc04")
Arrays.asList("09ed51c3d5ac2099ded1d0e8cf8ee183")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
}
@ -177,7 +177,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("d588179e2d9ed6e92a6ae1a80ac04270")
Arrays.asList("9d233d3d8cec8e580acb98b1a2725b56")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}
@ -198,7 +198,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("ceb0f5d9e0ea99eb8d00bce2f7bc1b73")
Arrays.asList("850094f32657f04cb958891de4cfc5b2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
}
@ -228,7 +228,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("94ce29b34b9e2e4304fc1bbf3f971a7d")
Arrays.asList("cea071b8b0ebd8f138ba91375edf036e")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
}
@ -259,7 +259,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("96de32970b204816ecd9a120b9d8782b")
Arrays.asList("e2f505046251e19b5737f4999c896fe2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
}
@ -292,7 +292,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("aea882132eb6afdc93fbc70e8d6c50e2")
Arrays.asList("8b97fe8e5e75efe08c080bbf47960c8f")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
}
@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("2a6215c86918a2f5c6748dd74057e79e")
Arrays.asList("1687108ed96d1127b196c2d74cf80a49")
);
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
}
@ -334,7 +334,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("0eed0ea48cb55164ba8d9383b96811c9"));
1, Arrays.asList("b1cace2d6c5932a9a85f41fc10e607b4"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
}
@ -365,8 +365,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000 -ST CpG", "60bbf3539212ff4ecb172e0ef848b297");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25");
expectations.put("-L 1:1-10,000,000 -ST CpG", "2a93c62ed4e062c043b7cc6dd0fa55f9");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "aade8425705c8870adb9d3fd67cae555");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -389,9 +389,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
expectations.put("", "226cfe7bf3fd7d2d0325b92c5b46619d");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "4965bd64de94b43daaa0ac2d296e9926");
expectations.put(" -knownName comp_hapmap", "98ba082dfff25ecff506ce03126f32da");
expectations.put("", "fc552fc9a02ac0d2327d73c375aab45e");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "09496523136290628bdc233f03ac9a38");
expectations.put(" -knownName comp_hapmap", "8ad493a6427673ca6835303b41f40897");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
@ -409,7 +409,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV 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";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2b969088abbfe69337fc3af663278323"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e83edc273504f5ea11de329f81af3de6"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
}
@ -444,7 +444,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -D " + dbsnp +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9cc6b8df93341cf391c1cb9ad0ef6df2"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("5d0d89c7cbcc7887e34447cee70c5bae"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -458,7 +458,7 @@ 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("77ffc1b12bff90a993842a0eeed450ba"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("8dec8f384852876ba8ec4943ff953d2d"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}