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Added UnitTests for getFamilies() and getChildrenWithParents()

This commit is contained in:
Laurent Francioli 2011-12-09 15:57:07 +01:00
parent 5a06170804
commit 72fbfba97d
1 changed files with 62 additions and 0 deletions
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62
public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
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@ -27,11 +27,42 @@ public class SampleDBUnitTest extends BaseTest {
new Sample("dad", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED),
new Sample("mom", "fam1", null, null, Gender.FEMALE, Affection.AFFECTED)));
private static final Set<Sample> testPEDFamilyF2 = new HashSet<Sample>(Arrays.asList(
new Sample("s2", "fam2", "d2", "m2", Gender.FEMALE, Affection.AFFECTED),
new Sample("d2", "fam2", null, null, Gender.MALE, Affection.UNKNOWN),
new Sample("m2", "fam2", null, null, Gender.FEMALE, Affection.UNKNOWN)
));
private static final Set<Sample> testPEDFamilyF3 = new HashSet<Sample>(Arrays.asList(
new Sample("s1", "fam3", "d1", "m1", Gender.FEMALE, Affection.AFFECTED),
new Sample("d1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN),
new Sample("m1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN)
));
private static final Set<Sample> testSAMSamples = new HashSet<Sample>(Arrays.asList(
new Sample("kid", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN),
new Sample("mom", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN),
new Sample("dad", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN)));
private static final HashMap<String, Set<Sample>> testGetFamilies = new HashMap<String,Set<Sample>>();
static {
testGetFamilies.put("fam1", testPEDSamples);
testGetFamilies.put("fam2", testPEDFamilyF2);
testGetFamilies.put("fam3", testPEDFamilyF3);
}
private static final Set<Sample> testKidsWithParentsFamilies2 = new HashSet<Sample>(Arrays.asList(
new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED),
new Sample("kid3", "fam5", "dad2", "mom2", Gender.MALE, Affection.AFFECTED),
new Sample("kid2", "fam5", "dad2", "mom2", Gender.MALE, Affection.AFFECTED)));
private static final HashSet<String> testGetPartialFamiliesIds = new HashSet<String>(Arrays.asList("kid","s1"));
private static final HashMap<String, Set<Sample>> testGetPartialFamilies = new HashMap<String,Set<Sample>>();
static {
testGetPartialFamilies.put("fam1", new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED))));
testGetPartialFamilies.put("fam3", new HashSet<Sample>(Arrays.asList(new Sample("s1", "fam3", "d1", "m1", Gender.FEMALE, Affection.AFFECTED))));
}
private static final String testPEDString =
String.format("%s%n%s%n%s",
"fam1 kid dad mom 1 2",
@ -46,6 +77,18 @@ public class SampleDBUnitTest extends BaseTest {
"fam3 s1 d1 m1 2 2",
"fam2 s2 d2 m2 2 2");
private static final String testPEDMultipleFamilies2 =
String.format("%s%n%s%n%s%n%s%n%s%n%s%n%s%n%s%n%s",
"fam1 kid dad mom 1 2",
"fam1 dad 0 0 1 1",
"fam1 mom 0 0 2 2",
"fam4 kid4 dad4 0 1 2",
"fam4 dad4 0 0 1 1",
"fam5 kid2 dad2 mom2 1 2",
"fam5 kid3 dad2 mom2 1 2",
"fam5 dad2 0 0 1 1",
"fam5 mom2 0 0 2 2");
private static final String testPEDStringInconsistentGender =
"fam1 kid 0 0 2 2";
@ -138,6 +181,25 @@ public class SampleDBUnitTest extends BaseTest {
Assert.assertEquals(db.getFamily("fam1"), testPEDSamplesAsSet);
}
@Test()
public void getFamilies(){
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
SampleDB db = builder.getFinalSampleDB();
Assert.assertEquals(db.getFamilies(),testGetFamilies);
Assert.assertEquals(db.getFamilies(null),testGetFamilies);
Assert.assertEquals(db.getFamilies(testGetPartialFamiliesIds),testGetPartialFamilies);
}
@Test()
public void testGetChildrenWithParents()
{
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
SampleDB db = builder.getFinalSampleDB();
Assert.assertEquals(db.getChildrenWithParents(), testKidsWithParentsFamilies2);
Assert.assertEquals(db.getChildrenWithParents(false), testKidsWithParentsFamilies2);
Assert.assertEquals(db.getChildrenWithParents(true), new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED))));
}
@Test()
public void loadFamilyIDs() {
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));