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Added function to get founders IDs in SampleDB 

Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
This commit is contained in:
Laurent Francioli 2012-04-25 16:27:38 +02:00 committed by Eric Banks
parent 120deaa010
commit 19d5213d5a
2 changed files with 17 additions and 0 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
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@ -235,4 +235,14 @@ public class SampleDB {
}
return children;
}
public Set<String> getFounderIds(){
Set<String> founders = new HashSet<String>();
for(Sample sample : getSamples()){
if(sample.getParents().size()<1)
founders.add(sample.getID());
}
return founders;
}
}

7
public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
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@ -200,6 +200,13 @@ public class SampleDBUnitTest extends BaseTest {
Assert.assertEquals(db.getChildrenWithParents(true), new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED))));
}
@Test()
public void testGetFounderIds(){
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
SampleDB db = builder.getFinalSampleDB();
Assert.assertEquals(db.getFounderIds(), new HashSet<String>(Arrays.asList("dad","mom","dad2","mom2","dad4")));
}
@Test()
public void loadFamilyIDs() {
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));