if (variant.getLength() % 3 == 0) {
if (start != end && getLengthReference() != getReference().length() && getLength() != UNKNOWN_LENGTH) { sb.append("-"); if (sv != null && (sv.getCiEndLeft() != null || sv.getCiEndRight() != null)) {
if (variant.getLength() % 3 == 0) {
if (variant.getLength() % 3 == 0) {
public Integer getLengthReference() { return VariantBuilder.getLengthReference(getReference(), getType(), getLength()); }
if (variant.getLength() % 3 == 0) {
public Integer getLengthAlternate() { return VariantBuilder.getLengthAlternate(getAlternate(), getType(), getLength()); }
if (!variant.getLength().equals(Variant.UNKNOWN_LENGTH)) { if (variant.getAlternate().length() % 3 == 0) { SoNames.add(VariantAnnotationUtils.INFRAME_INSERTION);
if (!variant.getLength().equals(Variant.UNKNOWN_LENGTH)) { if (variant.getAlternate().length() % 3 == 0) { SoNames.add(VariantAnnotationUtils.INFRAME_INSERTION);
public void transformToEnsemblFormat() { if (getType() == VariantType.INDEL || getType() == VariantType.SV || getLength() > 1) { if (getReference().charAt(0) == getAlternate().charAt(0)) { setReference(getReference().substring(1)); setAlternate(getAlternate().substring(1)); setStart(getStart() + 1); if (getReference().length() < getAlternate().length()) { setEnd(getEnd() - 1); } if (getReference().equals("")) { setReference("-"); } if (getAlternate().equals("")) { setAlternate("-"); } resetLength(); } } }
@Override public List<String> buildAlleles(Variant variant, Pair<Integer, Integer> adjustedRange, Map<Integer, Character> referenceAlleles) { String reference = variant.getReference(); String alternate = variant.getAlternate(); if (variant.getSv() != null && variant.getSv().getType() == StructuralVariantType.TANDEM_DUPLICATION && alternate.equals(VariantBuilder.DUP_ALT)) { alternate = VariantBuilder.DUP_TANDEM_ALT; } if (variant.getType().equals(VariantType.NO_VARIATION)) { return Arrays.asList(reference, "."); } StudyEntry study = getStudy(variant); List<AlternateCoordinate> secAlts = study.getSecondaryAlternates(); List<String> alleles = new ArrayList<>(secAlts.size() + 2); int origStart = variant.getStart(); int origEnd; if (variant.getLength() == Variant.UNKNOWN_LENGTH) { // Variant::getLengthReference would return UNKNOWN_LENGTH, as the reference could have incomplete reference length origEnd = variant.getStart() + variant.getReference().length() - 1; } else { origEnd = variant.getEnd(); } alleles.add(buildAllele(variant.getChromosome(), origStart, origEnd, reference, adjustedRange, referenceAlleles)); alleles.add(buildAllele(variant.getChromosome(), origStart, origEnd, alternate, adjustedRange, referenceAlleles)); secAlts.forEach(alt -> { int alternateStart = alt.getStart() == null ? variant.getStart() : alt.getStart().intValue(); int alternateEnd = alt.getEnd() == null ? variant.getEnd() : alt.getEnd().intValue(); alleles.add(buildAllele(variant.getChromosome(), alternateStart, alternateEnd, alt.getAlternate(), adjustedRange, referenceAlleles)); }); return alleles; }
} else if (normalizedVariant.getLength() == 1) { setRangeCoordsAndAlleles(normalizedVariant.getStart() - 1, normalizedVariant.getStart() - 1, normalizedVariant.getReference(), normalizedVariant.getAlternate(), transcript, hgvsStringBuilder); normalizedVariant.getStart() + normalizedVariant.getLength() - 1, normalizedVariant.getReference(), normalizedVariant.getAlternate(), transcript, hgvsStringBuilder);
} else if (normalizedVariant.getLength() == 1) { setRangeCoordsAndAlleles(normalizedVariant.getStart() - 1, normalizedVariant.getStart() - 1, normalizedVariant.getReference(), normalizedVariant.getAlternate(), transcript, hgvsStringBuilder); normalizedVariant.getStart() + normalizedVariant.getLength() - 1, normalizedVariant.getReference(), normalizedVariant.getAlternate(), transcript, hgvsStringBuilder);
.append(DocumentToVariantConverter.START_FIELD, variant.getStart()) .append(DocumentToVariantConverter.END_FIELD, variant.getStart()) .append(DocumentToVariantConverter.LENGTH_FIELD, variant.getLength()) .append(DocumentToVariantConverter.REFERENCE_FIELD, variant.getReference()) .append(DocumentToVariantConverter.ALTERNATE_FIELD, variant.getAlternate())
private Variant convert(org.opencb.biodata.models.variant.Variant var) { Variant build = Variant.newBuilder() .setChromosome(var.getChromosome()) .setStart(var.getStart()) .setEnd(var.getEnd()) .setLength(var.getLength()) .setReference(var.getReference()) .setAlternate(var.getAlternate()) .addAllIds(var.getIds()) .build(); return build; }
.append(START_FIELD, variant.getStart()) .append(END_FIELD, variant.getEnd()) .append(LENGTH_FIELD, variant.getLength()) .append(REFERENCE_FIELD, variant.getReference()) .append(ALTERNATE_FIELD, variant.getAlternate())