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Merge pull request #800 from broadinstitute/ldg_CGPpedError 

Address user-reported bug featuring "trio" family with two children, one...
This commit is contained in:
rpoplin 2015-01-14 09:35:33 -05:00
parent cf4ac4a388 6b2bd5ed09
commit 8599132713
2 changed files with 18 additions and 2 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java
View File

@ -298,7 +298,7 @@ public class FamilyLikelihoodsUtils {
if(family.size() == 3){ if(family.size() == 3){
for(final Sample familyMember : family){ for(final Sample familyMember : family){
parents = familyMember.getParents(); parents = familyMember.getParents();
if(parents.size()>0){ if(parents.size()==2){
if(family.containsAll(parents)) if(family.containsAll(parents))
trios.add(familyMember); trios.add(familyMember);
} }

18
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
View File

@ -61,6 +61,8 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
private static String CEUtrioFamilyFile = privateTestDir + "CEUtrio.ped"; private static String CEUtrioFamilyFile = privateTestDir + "CEUtrio.ped";
private static String CEUtrioTest = privateTestDir + "CEUtrioTest.vcf"; private static String CEUtrioTest = privateTestDir + "CEUtrioTest.vcf";
private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.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) @Test(enabled = true)
//use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000 //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); 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);
}
}
}