Examples with AlleleList org.broadinstitute.hellbender.utils.genotyper.AlleleList used on opensource projects

Example 1 with AlleleList

use of org.broadinstitute.hellbender.utils.genotyper.AlleleList in project gatk by broadinstitute.

the class RMSMappingQualityUnitTest method testLikelihoodsEmpty_AS.

@Test
public void testLikelihoodsEmpty_AS() throws Exception {
    final List<GATKRead> reads = Collections.emptyList();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.create("A")));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new AS_RMSMappingQuality().annotate(referenceContext, vc, likelihoods);
    final String[] split = ((String) annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AS_RMSMappingQuality.SPLIT_DELIM);
    Assert.assertEquals(split.length, 2);
    Assert.assertEquals(split[0], String.format("%.2f", 0.0));
    Assert.assertEquals(split[1], String.format("%.2f", 0.0));
}

Example 2 with AlleleList

use of org.broadinstitute.hellbender.utils.genotyper.AlleleList in project gatk by broadinstitute.

the class RMSMappingQualityUnitTest method testEmptyLikelihoods.

@Test
public void testEmptyLikelihoods() throws Exception {
    final List<GATKRead> reads = Collections.emptyList();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.create("A")));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new RMSMappingQuality().annotate(referenceContext, vc, likelihoods);
    Assert.assertTrue(annotate.isEmpty());
}

Example 3 with AlleleList

use of org.broadinstitute.hellbender.utils.genotyper.AlleleList in project gatk by broadinstitute.

the class MappingQualityZeroUnitTest method testEmptyLikelihoods.

@Test
public void testEmptyLikelihoods() throws Exception {
    final List<GATKRead> reads = Collections.emptyList();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.create("A")));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new MappingQualityZero().annotate(referenceContext, vc, likelihoods);
    //strangely,  MappingQualityZero returns 0 if likelihoods is empty
    final int n = 0;
    Assert.assertEquals(annotate.get(VCFConstants.MAPPING_QUALITY_ZERO_KEY), String.valueOf(n));
}

Example 4 with AlleleList

use of org.broadinstitute.hellbender.utils.genotyper.AlleleList in project gatk by broadinstitute.

the class CoverageUnitTest method testLikelihoodsEmpty.

@Test
public void testLikelihoodsEmpty() throws Exception {
    final List<GATKRead> reads = new ArrayList<>();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.NO_CALL));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new Coverage().annotate(referenceContext, vc, likelihoods);
    Assert.assertTrue(annotate.isEmpty());
}

Example 5 with AlleleList

use of org.broadinstitute.hellbender.utils.genotyper.AlleleList in project gatk by broadinstitute.

the class HaplotypeBAMWriterUnitTest method generateReadLikelihoods.

private ReadLikelihoods<Haplotype> generateReadLikelihoods(final int[] readCount) {
    final AlleleList<Haplotype> haplotypeList = generateHaplotypeList();
    final SampleList sampleList = generateSampleList(readCount.length);
    final Map<String, List<GATKRead>> readSamples = new LinkedHashMap<>(readCount.length);
    for (int i = 0; i < readCount.length; i++) {
        readSamples.put(sampleList.getSample(i), generateReadsList(i, readCount[i]));
    }
    return new ReadLikelihoods<>(sampleList, haplotypeList, readSamples);
}