From b24cff780b2294d331b705cfec10ac615dc46815 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 27 May 2014 09:59:52 -0400 Subject: [PATCH] Removing HWP from GenotypeSummaries because of integer overflow issues with 91K samples. Removing CCC because it is redundant. --- .../walkers/annotator/GenotypeSummaries.java | 2 -- .../annotator/GenotypeSummariesUnitTest.java | 2 -- .../GenotypeGVCFsIntegrationTest.java | 16 ++++++++-------- 3 files changed, 8 insertions(+), 12 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java index 4ffffe9ab..4cd92c938 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java @@ -89,9 +89,7 @@ public class GenotypeSummaries extends InfoFieldAnnotation implements ActiveRegi return null; final Map returnMap = new HashMap<>(); - returnMap.put(CCC, vc.getCalledChrCount()); returnMap.put(NCC, vc.getNoCallCount()); - returnMap.put(HWP, String.format("%.4f", GATKVariantContextUtils.computeHardyWeinbergPvalue(vc))); final MathUtils.RunningAverage average = new MathUtils.RunningAverage(); for( final Genotype g : vc.getGenotypes() ) { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java index 73abacdda..09b0688ed 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java @@ -77,10 +77,8 @@ public class GenotypeSummariesUnitTest { final GenotypeSummaries GS = new GenotypeSummaries(); final Map resultMap = GS.annotate(null, null, null, null, testVC, null); - Assert.assertEquals(2, resultMap.get(GenotypeSummaries.CCC)); // 2 called chromosomes Assert.assertEquals(1, resultMap.get(GenotypeSummaries.NCC)); // 1 no-called called sample Assert.assertEquals(30.0, Double.parseDouble((String)resultMap.get(GenotypeSummaries.GQ_MEAN)), 1E-4); // mean GQ is 30 Assert.assertFalse(resultMap.containsKey(GenotypeSummaries.GQ_STDDEV)); // no stddev with only one data point - Assert.assertTrue(resultMap.containsKey(GenotypeSummaries.HWP)); } } 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 8c214ce5f..b2f6997bf 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 @@ -65,7 +65,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("09575e44c9dbcd171a30eff43961c57f")); + Arrays.asList("51bf72a5eb3b2592d319072e4ce26c92")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -77,7 +77,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -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("fc701a483e7f0672f8c9a189c7b53015")); + Arrays.asList("4200fce6f253ef51dc4cd903794270b9")); executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec); } @@ -90,7 +90,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("3f34e05318479cf8743f4227491c7cd1")); + Arrays.asList("46044467b366db1c15a48a429b7c2291")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } @@ -102,7 +102,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), 1, - Arrays.asList("dc13542c71fbb4846507b0cdcc4827be")); + Arrays.asList("52655b4a693bc79e1029e47276a2653b")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } @@ -112,7 +112,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf", 1, - Arrays.asList("afff9f7b03008214ad41d430d57bb541")); + Arrays.asList("6fe339b17f4e5621e849d842c64a6e42")); executeTest("testJustOneSample", spec); } @@ -123,7 +123,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V " + privateTestDir + "gvcfExample1.vcf" + " -V " + privateTestDir + "gvcfExample2.vcf", 1, - Arrays.asList("2b0f8662be950e49911dfd2d93776712")); + Arrays.asList("aad7bda0f3c60689b61e87d641b62856")); executeTest("testSamplesWithDifferentLs", spec); } @@ -134,12 +134,12 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf", 1, - Arrays.asList("97bf0aad80b3992704166bbaca0cc455")); + Arrays.asList("1dda31e020086a4c5643571fbccd40ba")); 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("97bf0aad80b3992704166bbaca0cc455")); + Arrays.asList("1dda31e020086a4c5643571fbccd40ba")); executeTest("testNoPLsException.1", spec1); executeTest("testNoPLsException.2", spec2); }