@Deprecated public static VariantType inferType(String reference, String alternate) { return VariantBuilder.inferType(reference, alternate); }
public void resetType() { setType(VariantBuilder.inferType(getReference(), getAlternate())); }
type = inferType(reference, alternates.get(0));
public List<AlternateCoordinate> getSecondaryAlternates(String chromosome, VariantKeyFields alternate, List<VariantKeyFields> reorderedKeyFields) { List<AlternateCoordinate> secondaryAlternates = new ArrayList<>(reorderedKeyFields.size()); for (VariantKeyFields keyFields : reorderedKeyFields) { if (!keyFields.equals(alternate)) { secondaryAlternates.add(new AlternateCoordinate( chromosome, keyFields.getStart(), keyFields.getEnd(), keyFields.getReference(), keyFields.getAlternate(), VariantBuilder.inferType(keyFields.getReference(), keyFields.getAlternate()) )); } } return secondaryAlternates; }
List<AlternateCoordinate> secondaryAlternates = new ArrayList<>(alternates.size() - 1); for (int i = 1; i < alternates.size(); i++) { secondaryAlternates.add(new AlternateCoordinate(chromosome, start, end, reference, alternates.get(i), inferType(reference, alternates.get(i))));
VariantType variantType = VariantBuilder.inferType(variantAnnotation.getReference(), variantAnnotation.getAlternate()); if (StringUtils.isNotBlank(variantAnnotation.getId())) { if (variantType.equals(VariantType.SNV)) {
/** * Get the variant as Alternate Coordinate. * * At this point, we don't care if the Alternate is SNP or SNV. * In case that the variant is SV, recalculate the type, just in case the size has changed. * * @param variant Variant * @return Variant as AlternateCoordinate */ public static AlternateCoordinate getMainAlternate(Variant variant) { VariantType type; switch (variant.getType()) { case SNP: type = VariantType.SNV; break; case MNP: type = VariantType.MNV; break; case SV: type = VariantBuilder.inferType(variant.getReference(), variant.getAlternate()); break; default: type = variant.getType(); } return new AlternateCoordinate(variant.getChromosome(), variant.getStart(), variant.getEnd(), variant.getReference(), variant.getAlternate(), type); }
.setReference(reference) .setAlternate(alternates.get(i)) .setType(getProtoVariantType(inferType(reference, alternates.get(i)))));