/**
* 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));
}
}
}
private static void assertAttributeEquals(
final String key, final Object actual, final Object expected) {
if (expected instanceof Double) {
// must be very tolerant because doubles are being rounded to 2 sig figs
VariantBaseTest.assertEqualsDoubleSmart(actual, (Double) expected, 1e-2);
} else Assert.assertEquals(actual, expected, "Attribute " + key);
}