Package org.broadinstitute.gatk.tools.walkers.genotyper

Examples of org.broadinstitute.gatk.tools.walkers.genotyper.SampleList

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        UAC.genotypingOutputMode = GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;

        String trackName = variantCollection.variants.getName();

        final GenomeAnalysisEngine toolkit = getToolkit();
        final SampleList samples =
                new IndexedSampleList(SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)));
        final Set<String> sampleNameSet = SampleListUtils.asSet(samples);
        UG_engine = new UnifiedGenotypingEngine(UAC, samples,toolkit.getGenomeLocParser(),
                FixedAFCalculatorProvider.createThreadSafeProvider(toolkit,UAC,logger),
                toolkit.getArguments().BAQMode);
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*/
public class SampleListUtilsUnitTest {

    @Test(dataProvider = "singleSampleListData")
    public void testAsList(final List<String> samples) {
         final SampleList sampleList = new IndexedSampleList(samples);
         final List<String> asList = SampleListUtils.asList(sampleList);
         Assert.assertEquals(samples, asList);
    }
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         Assert.assertEquals(samples, asList);
    }

    @Test(dataProvider = "twoSampleListData", dependsOnMethods={"testAsList"})
    public void testEquals(final List<String> sample2, final List<String> samples2) {
        final SampleList sampleList1 = new IndexedSampleList(sample2);
        final SampleList sampleList2 = new IndexedSampleList(samples2);
        Assert.assertTrue(SampleListUtils.equals(sampleList1, sampleList1));
        Assert.assertTrue(SampleListUtils.equals(sampleList2,sampleList2));
        Assert.assertEquals(SampleListUtils.equals(sampleList1, sampleList2),
                Arrays.equals(SampleListUtils.asList(sampleList1).toArray(new String[sampleList1.sampleCount()]),
                        SampleListUtils.asList(sampleList2).toArray(new String[sampleList2.sampleCount()]))
        );
        Assert.assertEquals(SampleListUtils.equals(sampleList1,sampleList2),
                            SampleListUtils.equals(sampleList2,sampleList1));
    }
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Related Classes of org.broadinstitute.gatk.tools.walkers.genotyper.SampleList

  • org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtilsUnitTest
  • org.broadinstitute.gatk.tools.walkers.variantutils.RegenotypeVariants
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