diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index 070fdaca4..77e4391a3 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -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 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 }