From e119feee619d689e74a0a400fbe2c84a0534dbc9 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Tue, 7 Jun 2016 10:36:03 -0400 Subject: [PATCH] Added regression test for genotyping of spanning deletions in GenotypeGCVFs. --- ...ferenceConfidenceVariantContextMerger.java | 10 +- .../GenotypeGVCFsIntegrationTest.java | 205 +++++++++--------- 2 files changed, 112 insertions(+), 103 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java index df9183f0e..5ad0c581c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java @@ -135,7 +135,7 @@ public class ReferenceConfidenceVariantContextMerger { // record whether it's also a spanning deletion/event (we know this because the VariantContext type is no // longer "symbolic" but "mixed" because there are real alleles mixed in with the symbolic non-ref allele) sawSpanningDeletion |= ( isSpanningEvent && vc.isMixed() ) || vc.getAlternateAlleles().contains(Allele.SPAN_DEL) || - vc.getAlternateAlleles().contains(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED ); + vc.getAlternateAlleles().contains(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED); sawNonSpanningEvent |= ( !isSpanningEvent && vc.isMixed() ); vcAndNewAllelePairs.add(new Pair<>(vc, isSpanningEvent ? replaceWithNoCallsAndDels(vc) : remapAlleles(vc, refAllele, finalAlleleSet))); @@ -186,7 +186,7 @@ public class ReferenceConfidenceVariantContextMerger { //annotatorEngine.combineAnnotations removed the successfully combined annotations, so now parse those that are left //here we're assuming that things that are left are scalars per sample - Map> parsedAnnotationMap = parseRemainingAnnotations(annotationMap); + final Map> parsedAnnotationMap = parseRemainingAnnotations(annotationMap); // when combining remaining annotations use the median value from all input VCs which had annotations provided for ( final Map.Entry> p : parsedAnnotationMap.entrySet() ) { @@ -469,11 +469,11 @@ public class ReferenceConfidenceVariantContextMerger { if (perSampleIndexesOfRelevantAlleles == null) throw new IllegalArgumentException("The per sample index of relevant alleles must not be null"); - final List sacIndexesToUse = new ArrayList(2 * perSampleIndexesOfRelevantAlleles.length); + final List sacIndexesToUse = new ArrayList<>(2 * perSampleIndexesOfRelevantAlleles.length); for (int item : perSampleIndexesOfRelevantAlleles) { - sacIndexesToUse.add(new Integer(2 * item)); - sacIndexesToUse.add(new Integer(2 * item + 1)); + sacIndexesToUse.add(2 * item); + sacIndexesToUse.add(2 * item + 1); } return sacIndexesToUse; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index 5c27031a0..56d506ce3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -66,7 +66,6 @@ import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.List; @@ -79,61 +78,61 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { return baseTestString(" -V " + privateTestDir + "gvcf.basepairResolution.vcf " + args, b37KGReference); } - @Test(enabled = true) + @Test public void testUpdatePGT() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference), 1, - Arrays.asList("8d9788afd0de26bd9d9e55dd0e9fc3ed")); + Collections.singletonList("8d9788afd0de26bd9d9e55dd0e9fc3ed")); executeTest("testUpdatePGT", spec); } - @Test(enabled = true) + @Test public void testUpdatePGTStrandAlleleCountsBySample() throws IOException{ - final String logFileName = new String("testUpdatePGTStrandAlleleCountsBySample.log"); - WalkerTestSpec spec = new WalkerTestSpec( + final String logFileName = "testUpdatePGTStrandAlleleCountsBySample.log"; + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference), 1, - Arrays.asList("5dd4698da963a423446bb1e183eb75aa")); + Collections.singletonList("5dd4698da963a423446bb1e183eb75aa")); executeTest("testUpdatePGTStrandAlleleCountsBySample", spec); - File file = new File(logFileName); + final File file = new File(logFileName); Assert.assertTrue(FileUtils.readFileToString(file).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG)); } - @Test(enabled = true) + @Test public void combineSingleSamplePipelineGVCF() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000", b37KGReference), 1, - Arrays.asList("c9edd4ca8c2801c4681322087d82e781")); + Collections.singletonList("c9edd4ca8c2801c4681322087d82e781")); executeTest("combineSingleSamplePipelineGVCF", spec); } - @Test(enabled = true) + @Test public void testTetraploidRun() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "tetraploid-gvcf-1.vcf" + " -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" + " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad")); + Collections.singletonList("64fa89f20ee25df21ad20ce4ada7e7ad")); executeTest("testTetraploidRun", spec); } - @Test(enabled= true) + @Test public void testMixedPloidyRun() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "haploid-gvcf-1.vcf" + " -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" + " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("b1d93f4cd93093c208be2c9842f38d12")); + Collections.singletonList("b1d93f4cd93093c208be2c9842f38d12")); executeTest("testMixedPloidyRun", spec); } @@ -146,121 +145,121 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -L " + privateTestDir + "tetraploid-gvcfs.intervals" + " -maxNumPLValues 3", b37KGReference), 1, - Arrays.asList("c0dcf62fb116c4c0baabe432eceea52c")); + Collections.singletonList("c0dcf62fb116c4c0baabe432eceea52c")); executeTest("testMixedPloidyMaxNumPLValuesRun", spec); } - @Test(enabled = true) + @Test public void combineSingleSamplePipelineGVCF_includeNonVariants() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference), 1, - Arrays.asList("c2f30f25ba4a84e38c04aa49b95694e8")); + Collections.singletonList("c2f30f25ba4a84e38c04aa49b95694e8")); executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec); } - @Test(enabled = true) + @Test public void combineSingleSamplePipelineGVCFHierarchical() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" + " -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("f48114bc6348cdc9dc4f0960f5dcf5f8")); + Collections.singletonList("f48114bc6348cdc9dc4f0960f5dcf5f8")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } - @Test(enabled = true) + @Test public void combineSingleSamplePipelineGVCF_addDbsnp() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), 1, - Arrays.asList("f88841deb5c2ce4f3bbea1e914a13898")); + Collections.singletonList("f88841deb5c2ce4f3bbea1e914a13898")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } - @Test(enabled = true) + @Test public void combineBPresGVCFs() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "NA12891.BPres.g.vcf" + " -V " + privateTestDir + "NA12892.BPres.g.vcf" + " -L 20:10433000-10436909", b37KGReference), 1, - Arrays.asList("f342872f485e6978501facc78c354078")); + Collections.singletonList("f342872f485e6978501facc78c354078")); executeTest("combineBPresGVCFs", spec); } - @Test(enabled = true) + @Test public void testJustOneSample() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf", 1, - Arrays.asList("9ff344a5ab87a2c3b128e435e2e86db0")); + Collections.singletonList("9ff344a5ab87a2c3b128e435e2e86db0")); executeTest("testJustOneSample", spec); } - @Test(enabled = true) + @Test public void testSamplesWithDifferentLs() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf" + " -V " + privateTestDir + "gvcfExample2.vcf", 1, - Arrays.asList("0c07ed795562ea96eab427e63a970384")); + Collections.singletonList("0c07ed795562ea96eab427e63a970384")); executeTest("testSamplesWithDifferentLs", spec); } - @Test(enabled = true) + @Test public void testNoPLsException() { // Test with input files with (1) 0/0 and (2) ./. final String md5 = "2f3d71272fdac19ac861cc7159edfb08"; - WalkerTestSpec spec1 = new WalkerTestSpec( + final WalkerTestSpec spec1 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf", 1, - Arrays.asList(md5)); - WalkerTestSpec spec2 = new WalkerTestSpec( + Collections.singletonList(md5)); + final WalkerTestSpec spec2 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.nocall.vcf", 1, - Arrays.asList(md5)); + Collections.singletonList(md5)); executeTest("testNoPLsException.1", spec1); executeTest("testNoPLsException.2", spec2); } @Test public void testNDA() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-nda"), 1, - Arrays.asList("ce064429e6cbcaa956d52ef22e102f2f")); + Collections.singletonList("ce064429e6cbcaa956d52ef22e102f2f")); executeTest("testNDA", spec); } @Test public void testMaxAltAlleles() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-maxAltAlleles 1"), 1, - Arrays.asList("1f1c0605fc8a500c9646132e0d7420a0")); + Collections.singletonList("1f1c0605fc8a500c9646132e0d7420a0")); executeTest("testMaxAltAlleles", spec); } @Test public void testStandardConf() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"), 1, - Arrays.asList("0283e784ed49bc2dce32a26137c43409")); + Collections.singletonList("0283e784ed49bc2dce32a26137c43409")); executeTest("testStandardConf", spec); } @@ -274,7 +273,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "--no_cmdline_in_header -o %s -L 20:10130000-10134800 " + "-ERC GVCF --sample_name NA12878 -variant_index_type LINEAR " + "-variant_index_parameter 128000 -A StrandAlleleCountsBySample", - 1, Arrays.asList("") + 1, Collections.singletonList("") ); specHaplotypeCaller.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC final File gVCF = executeTest("testStrandAlleleCountsBySampleHaplotypeCaller", specHaplotypeCaller).getFirst().get(0); @@ -283,7 +282,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference), 1, - Arrays.asList("34d76dc8dabc6a97e6d8f5365d7531e5")); + Collections.singletonList("34d76dc8dabc6a97e6d8f5365d7531e5")); spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC executeTest("testStrandAlleleCountsBySample", spec); } @@ -291,7 +290,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { @Test public void testUniquifiedSamples() throws IOException { //two copies of 5 samples; will also test InbreedingCoeff calculation for uniquified samples - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample1B " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + @@ -300,7 +299,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" + " --uniquifySamples", b37KGReference), 1, - Arrays.asList("16d7374502fa3cf99863d15d31b5ef86")); + Collections.singletonList("16d7374502fa3cf99863d15d31b5ef86")); executeTest("testUniquifiedSamples", spec); } @@ -321,7 +320,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s)); codec.readHeader(lineIteratorVCF); - List attributeValues = new ArrayList(); + final List attributeValues = new ArrayList(); while (lineIteratorVCF.hasNext()) { final String line = lineIteratorVCF.next(); Assert.assertFalse(line == null); @@ -352,7 +351,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3, 1, - Arrays.asList("")); + Collections.singletonList("")); genotypeBase.disableShadowBCF(); final File genotypeBaseVCF = executeTest("genotypeBase", genotypeBase).getFirst().get(0); final List BASE_VARIANT_CONTEXTS = getVariantContexts(genotypeBaseVCF); @@ -362,14 +361,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + gvcf1 + " -V " + gvcf2, 1, - Arrays.asList("")); + Collections.singletonList("")); combine12.disableShadowBCF(); final File combined_gVCF12 = executeTest("combine12", combine12).getFirst().get(0); final WalkerTestSpec genotype12_3 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF12.getAbsolutePath() + " -V " + gvcf3, 1, - Arrays.asList("")); + Collections.singletonList("")); genotype12_3.disableShadowBCF(); final File genotype12_3VCF = executeTest("genotype12_3", genotype12_3).getFirst().get(0); final List VARIANT_CONTEXTS_12_3 = getVariantContexts(genotype12_3VCF); @@ -380,14 +379,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF12 + " -V " + gvcf3, 1, - Arrays.asList("")); + Collections.singletonList("")); combine12then3.disableShadowBCF(); final File combined_gVCF12then3 = executeTest("combined_gVCF12then3", combine12then3).getFirst().get(0); final WalkerTestSpec genotype12then3 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF12then3.getAbsolutePath(), 1, - Arrays.asList("")); + Collections.singletonList("")); genotype12then3.disableShadowBCF(); final File genotype12then3VCF = executeTest("genotype12then3", genotype12then3).getFirst().get(0); final List VARIANT_CONTEXTS_12then3 = getVariantContexts(genotype12then3VCF); @@ -398,21 +397,21 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + gvcf1 + " -V " + gvcf3, 1, - Arrays.asList("")); + Collections.singletonList("")); combine13.disableShadowBCF(); final File combined_gVCF13 = executeTest("combine13", combine13).getFirst().get(0); final WalkerTestSpec combine13then2 = new WalkerTestSpec( "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF13 + " -V " + gvcf2, 1, - Arrays.asList("")); + Collections.singletonList("")); combine13then2.disableShadowBCF(); final File combined_gVCF13then2 = executeTest("combined_gVCF13then2", combine13then2).getFirst().get(0); final WalkerTestSpec genotype13then2 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF13then2.getAbsolutePath(), 1, - Arrays.asList("")); + Collections.singletonList("")); genotype13then2.disableShadowBCF(); final File genotype13then2VCF = executeTest("genotype13then2", genotype13then2).getFirst().get(0); final List VARIANT_CONTEXTS_13then2 = getVariantContexts(genotype13then2VCF); @@ -423,14 +422,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3, 1, - Arrays.asList("")); + Collections.singletonList("")); combine123.disableShadowBCF(); final File combined_gVCF123 = executeTest("combine123", combine123).getFirst().get(0); final WalkerTestSpec genotype123 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + combined_gVCF123.getAbsolutePath(), 1, - Arrays.asList("")); + Collections.singletonList("")); genotype123.disableShadowBCF(); final File genotype123VCF = executeTest("genotype123", genotype123).getFirst().get(0); final List VARIANT_CONTEXTS_123 = getVariantContexts(genotype123VCF); @@ -474,113 +473,114 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82"; - @Test(enabled = true) + @Test public void testSpanningDeletionsMD5() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf", 1, - Arrays.asList(simpleSpanningDeletionsMD5)); + Collections.singletonList(simpleSpanningDeletionsMD5)); spec.disableShadowBCF(); executeTest("testSpanningDeletionsMD5", spec); } - @Test(enabled = true) + @Test public void testSpanningDeletionsFromCombinedGVCF() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.combined.g.vcf", 1, - Arrays.asList(simpleSpanningDeletionsMD5)); + Collections.singletonList(simpleSpanningDeletionsMD5)); spec.disableShadowBCF(); executeTest("testSpanningDeletionsFromCombinedGVCFMD5", spec); } - @Test(enabled = true) + @Test public void testMultipleSpanningDeletionsMD5() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf", 1, - Arrays.asList("7fe5364565585d31a0bb6a9dfa4a01d4")); + Collections.singletonList("7fe5364565585d31a0bb6a9dfa4a01d4")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsMD5", spec); } - @Test(enabled = true) + @Test public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.delOnly.g.vcf", 1, - Arrays.asList("057f9368f380bf3c12b539a749deac61")); + Collections.singletonList("057f9368f380bf3c12b539a749deac61")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } - @Test(enabled = true) + @Test public void testDeprecatedSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf", 1, - Arrays.asList("e8f5186718050fe0784416e41425563f")); + Collections.singletonList("e8f5186718050fe0784416e41425563f")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } - @Test(enabled = true) + @Test public void testGenotypingSpanningDeletionOverSpan() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.delOverSpan.1.g.vcf -V " + privateTestDir + "spanningDel.delOverSpan.2.g.vcf", 0, - Arrays.asList("")); // we do not care about the md5; we just want to make sure it doesn't blow up with an error + Collections.singletonList("")); // we do not care about the md5; we just want to make sure it doesn't blow up with an error spec.disableShadowBCF(); executeTest("testGenotypingSpanningDeletionOverSpan", spec); } - @Test(enabled = true) + @Test public void testBadADPropagationHaploidBugTest() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "ad-bug-input.vcf", 1, - Arrays.asList("5ed5cb6aac68aa8943dc45b8b90eb508")); + Collections.singletonList("5ed5cb6aac68aa8943dc45b8b90eb508")); spec.disableShadowBCF(); executeTest("testBadADPropagationHaploidBugTest", spec); } - @Test(enabled = true) + @Test public void testSAC() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf", 1, - Arrays.asList("37eec6aedd26aa3430a15d90d7f8a011")); + Collections.singletonList("37eec6aedd26aa3430a15d90d7f8a011")); spec.disableShadowBCF(); executeTest("testSAC", spec); } - @Test(enabled = true) + @Test public void testSACMultisampleTetraploid() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf", 1, - Arrays.asList("76532a74d4ba49f23362c149ad31a229")); + Collections.singletonList("76532a74d4ba49f23362c149ad31a229")); spec.disableShadowBCF(); executeTest("testSACMultisampleTetraploid", spec); } - @Test(enabled = true) + @Test public void testSetZeroRGQsToNoCall() { - WalkerTestSpec spec = new WalkerTestSpec( + final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" + " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" + " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames), - Arrays.asList("b7106be316e43ca04204b78038f65c9f")); + Collections.singletonList("b7106be316e43ca04204b78038f65c9f")); + spec.disableShadowBCF(); executeTest("testSetZeroRGQsToNoCall", spec); } @@ -588,7 +588,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("89712a9fe5b6db16be2257be2b0b4759")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("89712a9fe5b6db16be2257be2b0b4759")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -597,7 +597,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASMateRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V " + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e41a139600ab58a67910cdc60053726")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8e41a139600ab58a67910cdc60053726")); spec.disableShadowBCF(); executeTest("testASMateRankSumAnnotation", spec); } @@ -606,7 +606,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASInsertSizeRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b1334fbfbf21934aac1c1eda0b5062d5")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b1334fbfbf21934aac1c1eda0b5062d5")); spec.disableShadowBCF(); executeTest("testASInsertSizeRankSumAnnotation", spec); } @@ -619,7 +619,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_oneSample() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("7d86260e91fe74588e01339a2064b59c")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("7d86260e91fe74588e01339a2064b59c")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_oneSample", spec); } @@ -629,7 +629,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_elevenSamples() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "multiSamples.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a889fe6775575513e84905b4fa98f8b3")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("a889fe6775575513e84905b4fa98f8b3")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_elevenSamples", spec); } @@ -652,4 +652,13 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { executeTest("testAlleleSpecificAnnotations", spec); } + //Regression test for https://github.com/broadinstitute/gsa-unstable/issues/1281 + @Test + public void testGenotypingSpanningDeletionWithAllSites() { + final WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -V " + privateTestDir + "spanningDel.genotyping.g.vcf -allSites", b37KGReference), + Collections.singletonList("7cc3b08a37ed0c2e556debc1023cff2b")); + spec.disableShadowBCF(); + executeTest("testGenotypingSpanningDeletionWithAllSites", spec); + } } \ No newline at end of file