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

Example 1 with ReadLikelihoods

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

the class RMSMappingQualityUnitTest method testLikelihoods.

@Test
public void testLikelihoods() {
    final Allele REF = Allele.create("A", true);
    final Allele ALT = Allele.create("C", true);
    final int[] MQs = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, QualityUtils.MAPPING_QUALITY_UNAVAILABLE };
    final List<Integer> MQsList = Arrays.asList(ArrayUtils.toObject(MQs));
    //MQ 255 are excluded from the calculations, we test it here.
    final List<Integer> MQsListOK = new ArrayList<>(MQsList);
    //NOTE: if we just call remove(i), Java thinks i is an index.
    //A workaround for this overloading bogosity to to call removeAll and pass a collection
    //(casting i to (Object) would work too but it's more error prone)
    MQsListOK.removeAll(Collections.singleton(QualityUtils.MAPPING_QUALITY_UNAVAILABLE));
    final List<GATKRead> reads = Arrays.stream(MQs).mapToObj(mq -> AnnotationArtificialData.makeRead(20, mq)).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods("sample1", reads, -1.0, REF, ALT);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new RMSMappingQuality().annotate(referenceContext, vc, likelihoods);
    Assert.assertEquals(annotate.size(), 1, "size");
    Assert.assertEquals(annotate.keySet(), Collections.singleton(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), "annots");
    //only those are MQ0
    final double rms = MathUtils.sumOfSquares(MQsListOK);
    Assert.assertNull(annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY));
    Assert.assertEquals(annotate.get(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms));
}

Example 2 with ReadLikelihoods

use of org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods 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 3 with ReadLikelihoods

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

the class RMSMappingQualityUnitTest method testLikelihoods_AS.

@Test
public void testLikelihoods_AS() {
    final Allele REF = Allele.create("A", true);
    final Allele ALT = Allele.create("C");
    final int[] MQs = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, QualityUtils.MAPPING_QUALITY_UNAVAILABLE };
    final List<Integer> MQsList = Arrays.asList(ArrayUtils.toObject(MQs));
    //MQ 255 are excluded from the calculations, we test it here.
    final List<Integer> MQsListOK = new ArrayList<>(MQsList);
    //NOTE: if we just call remove(i), Java thinks i is an index.
    //A workaround for this overloading bogosity to to call removeAll and pass a collection
    //(casting i to (Object) would work too but it's more error prone)
    MQsListOK.removeAll(Collections.singleton(QualityUtils.MAPPING_QUALITY_UNAVAILABLE));
    final List<GATKRead> reads = Arrays.stream(MQs).mapToObj(mq -> AnnotationArtificialData.makeRead(30, mq)).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods("sample1", reads, -10.0, REF, ALT);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new AS_RMSMappingQuality().annotateRawData(referenceContext, vc, likelihoods);
    Assert.assertEquals(annotate.size(), 1, "size");
    Assert.assertEquals(annotate.keySet(), Collections.singleton(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY), "annots");
    //only those are MQ0
    final double rms = MathUtils.sumOfSquares(MQsListOK);
    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", rms));
    Assert.assertEquals(split[1], String.format("%.2f", 0.0));
}

Example 4 with ReadLikelihoods

use of org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods 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 5 with ReadLikelihoods

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

the class AS_StrandBiasTest method getStrandCountsFromLikelihoodMap.

/**
     Allocate and fill a 2x2 strand contingency table.  In the end, it'll look something like this:
     *             fw      rc
     *   allele1   #       #
     *   allele2   #       #
     * @return a 2x2 contingency table
     */
public void getStrandCountsFromLikelihoodMap(final VariantContext vc, final ReadLikelihoods<Allele> likelihoods, final ReducibleAnnotationData<List<Integer>> perAlleleValues, final int minCount) {
    if (likelihoods == null || vc == null) {
        return;
    }
    final Allele ref = vc.getReference();
    final List<Allele> allAlts = vc.getAlternateAlleles();
    for (final String sample : likelihoods.samples()) {
        final ReducibleAnnotationData<List<Integer>> sampleTable = new AlleleSpecificAnnotationData<>(vc.getAlleles(), null);
        likelihoods.bestAlleles(sample).stream().filter(ba -> ba.isInformative()).forEach(ba -> updateTable(ba.allele, ba.read, ref, allAlts, sampleTable));
        if (passesMinimumThreshold(sampleTable, minCount)) {
            combineAttributeMap(sampleTable, perAlleleValues);
        }
    }
}