@Test(expectedExceptions = IllegalArgumentException.class)
public void testAllNull() throws Exception {
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = null;
final VariantContext vc = null;
final ReferenceContext referenceContext = null;
final InfoFieldAnnotation cov = new RMSMappingQuality();
final Map<String, Object> annotate =
cov.annotate(referenceContext, vc, perReadAlleleLikelihoodMap); // vc can't be null
}
@Test
public void testNullStratifiedPerReadAlleleLikelihoodMap() throws Exception {
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = null;
final VariantContext vc = makeVC();
final ReferenceContext referenceContext = null;
final InfoFieldAnnotation cov = new RMSMappingQuality();
final Map<String, Object> annotate =
cov.annotate(referenceContext, vc, perReadAlleleLikelihoodMap);
Assert.assertNull(annotate);
Assert.assertEquals(cov.getDescriptions().size(), 1);
Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
}
@Test
public void testDescriptions() throws Exception {
final InfoFieldAnnotation cov = new RMSMappingQuality();
Assert.assertEquals(cov.getDescriptions().size(), 1);
Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
}
