@Test
public void calculateStats() throws Exception {

    this.ref = HBaseAlleleCalculatorTest.getVariant("Y:123:A:G", "2", 2, "S2", "0", HBaseAlleleCalculatorTest.map("FILTER", "not-pass"));
    this.snv = HBaseAlleleCalculatorTest.getVariant("Y:123:A:G", "2",  1, "S1", "1", HBaseAlleleCalculatorTest.map("FILTER", "not-pass"));
    this.singleStudyConfiguration = new StudyConfiguration(2, "2");
    this.singleStudyConfiguration.setIndexedFiles(new LinkedHashSet<>(Arrays.asList(1, 2)));
    this.singleStudyConfiguration.setSampleIds(HBaseAlleleCalculatorTest.mapObj("S2", 2, "S1", 1));
    this.singleStudyConfiguration.setFileIds(HBaseAlleleCalculatorTest.mapObj("file1", 1, "file2", 2));
    this.singleStudyConfiguration.setSamplesInFiles(HBaseAlleleCalculatorTest.mapObj(
            2, new LinkedHashSet<>(Collections.singleton(2)),
            1, new LinkedHashSet<>(Collections.singleton(1))));
    Configuration conf = new Configuration();
    VariantTableHelper.setInputTableName(conf, "input");
    VariantTableHelper.setOutputTableName(conf, "output");
    VariantTableHelper.setStudyId(conf, 2);
    this.variantTableHelper = new VariantTableHelper(conf);
    variantConverter = new HBaseAlleleCountsToVariantConverter(this.variantTableHelper, this.singleStudyConfiguration);
    this.variantConverter.setReturnSampleIds(Arrays.asList(1, 2));
    this.calculator = new HBaseAlleleCalculator("2", HBaseAlleleCalculatorTest.mapObj("S2", 2, "S1", 1));
    calculator.addVariant(snv);
    calculator.addVariant(ref);
    AlleleCountPosition validate = validate(new HashSet<Integer>(Arrays.asList(2)), snv,
            Collections.emptyMap(), HBaseAlleleCalculatorTest.mapObj(1, new HashSet<>(Arrays.asList(2))));
    Variant variant = convertBack(this.snv, validate);
    System.out.println("snv = " + snv.getImpl());
    equalsGT("S1", "1", variant);
    equalsGT("S2", "0", variant);
    AlleleStatsCalculator calculator = new AlleleStatsCalculator(Arrays.asList(1, 2));
    VariantStats stats = calculator.calculateStats(validate, new HashSet<>(Arrays.asList(1, 2)), variant);
    System.out.println("stats = " + stats);
    assertEquals(1, stats.getRefAlleleCount().intValue());
    assertEquals(1, stats.getAltAlleleCount().intValue());
}