From 6b2bd5ed09be06c47957424430a001737ef20535 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Tue, 13 Jan 2015 16:09:40 -0500 Subject: [PATCH] Address user-reported bug featuring "trio" family with two children, one parent Add test to cover case with family of one parent, two children --- .../variantutils/FamilyLikelihoodsUtils.java | 2 +- ...ulateGenotypePosteriorsIntegrationTest.java | 18 +++++++++++++++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java index 25678665a..25bcd3ef8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java @@ -298,7 +298,7 @@ public class FamilyLikelihoodsUtils { if(family.size() == 3){ for(final Sample familyMember : family){ parents = familyMember.getParents(); - if(parents.size()>0){ + if(parents.size()==2){ if(family.containsAll(parents)) trios.add(familyMember); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 9b659a89b..7f860f343 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -61,6 +61,8 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { private static String CEUtrioFamilyFile = privateTestDir + "CEUtrio.ped"; private static String CEUtrioTest = privateTestDir + "CEUtrioTest.vcf"; private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.vcf"; + private static String threeMemberNonTrioFamilyFile = privateTestDir + "threeMemberNonTrio.ped"; + private static String getThreeMemberNonTrioTest = privateTestDir + "threeMemberNonTrioTest.vcf"; @Test(enabled = true) //use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000 @@ -119,5 +121,19 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { executeTest("testFamilyPriors", spec); } + @Test(enabled = true) + public void testSingleParentFamily() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T CalculateGenotypePosteriors --no_cmdline_in_header " + + " -o %s" + + " -R " + b37KGReference + + " -ped " + threeMemberNonTrioFamilyFile + + " -V " + getThreeMemberNonTrioTest + + " -skipPop", + 1, + Arrays.asList("abfa4332bce9aba911ad2eba34ee9924")); + executeTest("testFamilyPriors", spec); + } -} \ No newline at end of file + +}