@Test
public void testPerReadAlleleLikelihoodMap() {
final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap();
final Allele alleleA = Allele.create("A");
final double lik = -1.0; // ignored
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 int n1A = MQs.length;
for (int i = 0; i < n1A; i++) {
final GATKRead read = ArtificialReadUtils.createArtificialRead(TextCigarCodec.decode("10M"));
read.setMappingQuality(MQs[i]);
map.add(read, alleleA, lik);
}
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap =
Collections.singletonMap("sample1", map);
final VariantContext vc = makeVC();
final ReferenceContext referenceContext = null;
final Map<String, Object> annotate =
new RMSMappingQuality().annotate(referenceContext, vc, perReadAlleleLikelihoodMap);
Assert.assertEquals(annotate.size(), 1, "size");
Assert.assertEquals(
annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots");
final double rms = MathUtils.rms(MQsListOK); // only those are MQ0
Assert.assertEquals(
annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms));
}
private GATKRead makeSamRead(
final int uuid, final String name, final int start, final int length) {
return ArtificialReadUtils.createSamBackedReadWithUUID(new UUID(0, uuid), name, start, length);
}
@BeforeClass
public void init() {
header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}