Examples with GATKRead org.broadinstitute.hellbender.utils.read.GATKRead used on opensource projects

Example 51 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class StrandOddsRatioUnitTest method makeRead.

private GATKRead makeRead(final boolean forward) {
    Cigar cigar = TextCigarCodec.decode("10M");
    final GATKRead read = ArtificialReadUtils.createArtificialRead(cigar);
    read.setIsReverseStrand(!forward);
    return read;
}

Example 52 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class VariantAnnotatorEngineUnitTest method makeReadLikelihoods.

private ReadLikelihoods<Allele> makeReadLikelihoods(final int ref, final int alt, final Allele refAllele, final Allele altAllele, final String contig, final int position) {
    final List<GATKRead> reads = new ArrayList<>();
    for (int i = 0; i < alt; i++) {
        final GATKRead read = ArtificialReadUtils.createUniqueArtificialRead("10M");
        read.setPosition(contig, position);
        reads.add(read);
    }
    for (int i = 0; i < ref; i++) {
        final GATKRead read = ArtificialReadUtils.createUniqueArtificialRead("10M");
        read.setPosition(contig, position);
        reads.add(read);
    }
    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(refAllele, altAllele));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    // modify likelihoods in-place
    final LikelihoodMatrix<Allele> matrix = likelihoods.sampleMatrix(0);
    int n = 0;
    for (int i = 0; i < alt; i++) {
        matrix.set(0, n, -100.0);
        matrix.set(1, n, -1.0);
        n++;
    }
    for (int i = 0; i < ref; i++) {
        matrix.set(0, n, -1.0);
        matrix.set(1, n, -100.0);
        n++;
    }
    return likelihoods;
}

Example 53 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead 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 54 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead 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 55 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead 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));
}