/** * Assert that two variant contexts are actually equal * * @param actual * @param expected */ public static void assertEquals(final VariantContext actual, final VariantContext expected) { Assert.assertNotNull(actual, "VariantContext expected not null"); Assert.assertEquals(actual.getChr(), expected.getChr(), "chr"); Assert.assertEquals(actual.getStart(), expected.getStart(), "start"); Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end"); Assert.assertEquals(actual.getID(), expected.getID(), "id"); Assert.assertEquals( actual.getAlleles(), expected.getAlleles(), "alleles for " + expected + " vs " + actual); assertAttributesEquals(actual.getAttributes(), expected.getAttributes()); Assert.assertEquals( actual.filtersWereApplied(), expected.filtersWereApplied(), "filtersWereApplied"); Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "isFiltered"); VariantBaseTest.assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters"); VariantBaseTest.assertEqualsDoubleSmart( actual.getPhredScaledQual(), expected.getPhredScaledQual()); Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes"); if (expected.hasGenotypes()) { VariantBaseTest.assertEqualsSet( actual.getSampleNames(), expected.getSampleNames(), "sample names set"); Assert.assertEquals( actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names"); final Set<String> samples = expected.getSampleNames(); for (final String sample : samples) { assertEquals(actual.getGenotype(sample), expected.getGenotype(sample)); } } }