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simpleMerge UnitTest for not annotating and annotating to different info key

This commit is contained in:
Mark DePristo 2011-09-22 17:26:11 -04:00
parent 30ab3af0c8
commit dab7232e9a
1 changed files with 20 additions and 4 deletions
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24
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
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@ -375,10 +375,26 @@ public class VariantContextUtilsUnitTest extends BaseTest {
Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
}
@Test
public void testAnnotationSet() {
for ( final boolean annotate : Arrays.asList(true, false)) {
for ( final String set : Arrays.asList("set", "combine", "x")) {
final List<String> priority = Arrays.asList("1", "2");
VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
Arrays.asList(vc1, vc2), priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false);
if ( annotate )
Assert.assertEquals(merged.getAttribute(set), VariantContextUtils.MERGE_INTERSECTION);
else
Assert.assertFalse(merged.hasAttribute(set));
}
}
}
// todo -- add tests for subset merging, especially with correct PLs
// todo -- test priority list: intersection, filtered in all, reference in all, X-filteredInX, X
// todo -- test FilteredRecordMergeType
// todo -- no annotate origin
// todo -- test set key
// todo -- test priority list
}