// Can't use Description, as that includes hypotheses that weren't necessarily called.
private static HashSet<String> extractCalledAlleles(final Variant variant) {
final HashSet<String> alleles = new HashSet<>();
for (int k = 0; k < variant.getNumberOfSamples(); k++) {
final VariantSample vs = variant.getSample(k);
if (vs != null) {
if (!vs.isIdentity()) {
Collections.addAll(alleles, StringUtils.split(vs.getName(), VariantUtils.COLON));
}
}
}
return alleles;
}
private static VariantSample[] createVariants(
final Variant original,
final int leftClip,
final int rightClip,
Description newDescription,
int[] alleleMapping) {
final VariantSample[] newSamples = new VariantSample[original.getNumberOfSamples()];
for (int k = 0; k < newSamples.length; k++) {
final VariantSample sample = original.getSample(k);
if (sample != null) {
final String newName = createVariantName(leftClip, rightClip, sample.getName());
newSamples[k] =
new VariantSample(
sample.getPloidy(),
newName,
sample.isIdentity(),
sample.getMeasure(),
sample.isDeNovo(),
sample.getDeNovoPosterior());
VariantSample.copy(sample, newSamples[k]);
// Update counts to correspond to the new description
final Description d =
newSamples[k].getStats().counts().getDescription() instanceof DescriptionNone
? DescriptionNone.SINGLETON
: newDescription;
newSamples[k].setStats((Statistics<?>) newSamples[k].getStats().copy());
newSamples[k].getStats().remapAlleleStatistics(d, alleleMapping);
final Map<Set<String>, Double> newMap = newGenotypeLikelihoods(leftClip, rightClip, sample);
newSamples[k].setGenotypeLikelihoods(newMap);
} else {
newSamples[k] = null;
}
}
return newSamples;
}
private static Map<Set<String>, Double> newGenotypeLikelihoods(
int leftClip, int rightClip, VariantSample sample) {
final Map<Set<String>, Double> newMap = new HashMap<>();
final Map<Set<String>, Double> originalLikelihoods = sample.getGenotypeLikelihoods();
if (originalLikelihoods != null) {
for (Map.Entry<Set<String>, Double> entry : originalLikelihoods.entrySet()) {
final Set<String> newSet = new HashSet<>();
for (String s : entry.getKey()) {
newSet.add(StringUtils.clip(s, leftClip, rightClip));
}
final Double v = newMap.get(newSet);
final double existing = v == null ? LogApproximatePossibility.SINGLETON.zero() : v;
newMap.put(newSet, LogApproximatePossibility.SINGLETON.add(existing, entry.getValue()));
}
return newMap;
} else {
return null;
}
}
/**
* changes the de novo flag from true to false on any sample incorrectly marked as de novo. (note
* does not do the opposite) Also deals with the somatic cause. Some variants after splitting will
* no longer have a somatic cause.
*
* @param variant the variant to check
* @param checker the de novo checker for the current inheritance scenario
* @return the corrected variant
*/
public static Variant denovoCorrect(DenovoChecker checker, Variant variant) {
final Set<Integer> nonDenovoSamples = new HashSet<>();
for (int s = 0; s < variant.getNumberOfSamples(); s++) {
final VariantSample sample = variant.getSample(s);
if (sample != null) {
final VariantSample.DeNovoStatus denovoCall = sample.isDeNovo();
if (denovoCall == VariantSample.DeNovoStatus.IS_DE_NOVO) {
if (!checker.isDenovo(variant, s)) {
nonDenovoSamples.add(s);
}
}
}
}
final Variant ret;
if (nonDenovoSamples.size() == 0) {
ret = variant;
} else {
final VariantLocus newLocus = variant.getLocus();
final VariantSample[] newSamples = new VariantSample[variant.getNumberOfSamples()];
for (int k = 0; k < newSamples.length; k++) {
final VariantSample sample = variant.getSample(k);
if (sample != null) {
final VariantSample.DeNovoStatus newStatus;
if (sample.isDeNovo() == VariantSample.DeNovoStatus.UNSPECIFIED) {
newStatus = VariantSample.DeNovoStatus.UNSPECIFIED;
} else {
newStatus =
sample.isDeNovo() == VariantSample.DeNovoStatus.IS_DE_NOVO
&& !nonDenovoSamples.contains(k)
? VariantSample.DeNovoStatus.IS_DE_NOVO
: VariantSample.DeNovoStatus.NOT_DE_NOVO;
}
newSamples[k] =
new VariantSample(
sample.getPloidy(),
sample.getName(),
sample.isIdentity(),
sample.getMeasure(),
newStatus,
sample.getDeNovoPosterior());
VariantSample.copy(sample, newSamples[k]);
}
}
final Variant newVariant = new Variant(newLocus, newSamples);
Variant.copy(variant, newVariant);
ret = newVariant;
}
return ret;
}