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Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants 

Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
This commit is contained in:
Guillermo del Angel 2011-08-20 12:24:22 -04:00
parent 0de49f5752
commit 782453235a
2 changed files with 22 additions and 20 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -344,11 +344,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
} }
// now, exclude any requested samples // now, exclude any requested samples
Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); if (XLsampleFiles != null)
samples.removeAll(XLsamplesFromFile); if(!XLsampleFiles.isEmpty()) {
samples.removeAll(XLsampleNames); Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
samples.removeAll(XLsamplesFromFile);
if ( samples.size() == 0 ) samples.removeAll(XLsampleNames);
}
if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
throw new UserException("All samples requested to be included were also requested to be excluded."); throw new UserException("All samples requested to be included were also requested to be excluded.");
for ( String sample : samples ) for ( String sample : samples )

30
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("bced1842c78fbabb089dd12b7087050d") Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec); executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
} }
@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("06510bd37ffaa39e817ca0dcaf8f8ac2") Arrays.asList("d470e00a368b5a0468012818994c6a89")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
} }
@ -72,7 +72,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("19c5b1b6396921c5b1059a2849ae4fcc") Arrays.asList("12856e52c2682328f91594089328596c")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
} }
@ -93,7 +93,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("a71f8d81cf166cd97ac628092650964a") Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
} }
@ -114,7 +114,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("4dabe0658232f6174188515db6dfe112") Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
} }
@ -135,7 +135,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("3340587f10ceff83e5567ddfd1a9a60e") Arrays.asList("15beaf3823c131cabc5fb0445239f978")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
} }
@ -156,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("c730c7ee31c8138cef6efd8dd04fbbfc") Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
} }
@ -179,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("2559ca8f454b03e81561f6947f79df18") Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
} }
@ -204,7 +204,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("23aa5f97641d2fd033095f21c51d2f37") Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
); );
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
} }
@ -223,7 +223,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("a69dd3f06903b3f374c6d6f010c653e0") Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
); );
executeTest("testFundamentalsCountVariantsNoCompRod", spec); executeTest("testFundamentalsCountVariantsNoCompRod", spec);
} }
@ -236,7 +236,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.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", WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("125fe0a04b5d933cc14016598b2791cd")); 1, Arrays.asList("2df4f8911ffc3c8d042298723ed465f8"));
executeTestParallel("testSelect1", spec); executeTestParallel("testSelect1", spec);
} }
@ -253,7 +253,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test @Test
public void testCompVsEvalAC() { 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"; 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("d1932be3748fcf6da77dc51aec323710")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ed54aa127b173d8ad8b6482f2a929a42"));
executeTestParallel("testCompVsEvalAC",spec); executeTestParallel("testCompVsEvalAC",spec);
} }
@ -283,7 +283,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --dbsnp " + b37dbSNP132 + " --dbsnp " + b37dbSNP132 +
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s"; " -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("cbea5f9f8c046d4c014d261db352c43b")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18c44636e36d6657110bf984f8eac181"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec); executeTestParallel("testEvalTrackWithoutGenotypes",spec);
} }
@ -295,7 +295,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s"; " -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d07a246963ae609643620c839b20cd1e")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1b8ae4fd10de0888bd843f833859d990"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
} }
@ -373,7 +373,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s" "-o %s"
), ),
1, 1,
Arrays.asList("44464fe7c89a56cf128a932ef640f7da") Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
); );
executeTest("testAlleleCountStrat", spec); executeTest("testAlleleCountStrat", spec);
} }