@Test(enabled=true)
public void testMissing() {
Pair<VariantContext,VariantContext> data = getData5();
VariantContext eval = data.getFirst();
VariantContext truth = data.getSecond();
VCFCodec codec = new VCFCodec();
VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
metrics.update(eval,truth);
Assert.assertTrue(eval.getGenotype("test1_sample2").getType().equals(GenotypeType.UNAVAILABLE));
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[0][2],0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[4][2],1);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][1],0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][3],0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][0],0);
Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][4],1);
}