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VariantEvalIntegrationTest for IntervalStratification

This commit is contained in:
Mark DePristo 2011-11-10 14:10:39 -05:00
parent 18f829f76b
commit 153e52ffed
1 changed files with 36 additions and 15 deletions
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51
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -70,7 +70,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
Arrays.asList("fb926edfd3d811e18b33798a43ef4379")
);
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
}
@ -91,7 +91,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("d470e00a368b5a0468012818994c6a89")
Arrays.asList("26b7d57e3a204ac80a28cb29485b59b7")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
}
@ -113,7 +113,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("12856e52c2682328f91594089328596c")
Arrays.asList("1df8184062f330bea9da8bacacc5a09d")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
}
@ -134,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
Arrays.asList("927f26414509db9e7c0a2c067d57c949")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
}
@ -155,7 +155,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
Arrays.asList("e6fddefd95122cabc5a0f0b95bce6d34")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}
@ -176,7 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("15beaf3823c131cabc5fb0445239f978")
Arrays.asList("df10486dae73a9cf8c647964f51ba3e0")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
}
@ -197,7 +197,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
Arrays.asList("524adb0b7ff70e227b8803a88f36713e")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
}
@ -220,7 +220,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
Arrays.asList("ef6449789dfc032602458b7c5538a1bc")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
}
@ -245,7 +245,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
Arrays.asList("13b90e94fa82d72bb04a0a5addb27c3f")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
}
@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
Arrays.asList("8458b9d7803d75aae551fac7dbd152d6")
);
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
}
@ -277,7 +277,7 @@ 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("f70997b6a3e7fdc89d11e1d61a2463d4"));
1, Arrays.asList("b954dee127ec4205ed7d33c91aa3e045"));
executeTestParallel("testSelect1", spec);
}
@ -294,7 +294,7 @@ 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("407682de41dcf139ea635e9cda21b912"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ae0027197547731a9a5c1eec5fbe0221"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -324,7 +324,7 @@ 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("424c9d438b1faa59b2c29413ba32f37b"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("835b44fc3004cc975c968c9f92ed25d6"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -336,7 +336,7 @@ 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("18fa0b89ebfff51141975d7e4ce7a159"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("f0e003f1293343c3210ae95e8936b19a"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@ -414,8 +414,29 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
Arrays.asList("924b6123edb9da540d0abc66f6f33e16")
);
executeTest("testAlleleCountStrat", spec);
}
@Test
public void testIntervalStrat() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + testDir + "/withSymbolic.b37.vcf",
"-noEV",
"-EV CountVariants",
"-noST",
"-stratIntervals " + testDir + "/overlapTest.bed",
"-ST IntervalStratification",
"-L 20",
"-o %s"
),
1,
Arrays.asList("9794e2dba205c6929dc89899fdf0bf6b")
);
executeTest("testIntervalStrat", spec);
}
}