public Integer getCopyNumber() { return sv == null ? null : sv.getCopyNumber(); }
public List<VariantKeyFields> normalizeSymbolic(final Integer start, final Integer end, final String reference, final List<String> alternates, StructuralVariation sv) { List<VariantKeyFields> list = new ArrayList<>(alternates.size()); int numAllelesIdx = 0; // This index is necessary for getting the samples where the mutated allele is present for (Iterator<String> iterator = alternates.iterator(); iterator.hasNext(); numAllelesIdx++) { String alternate = iterator.next(); VariantKeyFields keyFields; if (VariantBuilder.isMateBreakend(alternate)) { keyFields = normalizeMateBreakend(start, reference, alternate, alternates, numAllelesIdx); } else { Integer copyNumber = sv == null ? null : sv.getCopyNumber(); keyFields = normalizeSymbolic(start, end, reference, alternate, alternates, copyNumber, numAllelesIdx); } list.add(keyFields); } return list; }
private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant) throws UnsupportedURLVariantFormat { switch (VariantAnnotationUtils.getVariantType(variant)) { case SNV: return new ConsequenceTypeSNVCalculator(); case INSERTION: return new ConsequenceTypeInsertionCalculator(genomeDBAdaptor); case DELETION: return new ConsequenceTypeDeletionCalculator(genomeDBAdaptor); case MNV: return new ConsequenceTypeMNVCalculator(genomeDBAdaptor); case CNV: if (variant.getSv().getCopyNumber() == null) { return new ConsequenceTypeGenericRegionCalculator(); } else if (variant.getSv().getCopyNumber() > 2) { return new ConsequenceTypeCNVGainCalculator(); } else { return new ConsequenceTypeDeletionCalculator(genomeDBAdaptor); } case DUPLICATION: return new ConsequenceTypeCNVGainCalculator(); case INVERSION: return new ConsequenceTypeGenericRegionCalculator(); case BREAKEND: return new ConsequenceTypeBNDCalculator(); default: throw new UnsupportedURLVariantFormat(); } }
private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant) throws UnsupportedURLVariantFormat { switch (VariantAnnotationUtils.getVariantType(variant)) { case SNV: return new ConsequenceTypeSNVCalculator(); case INSERTION: return new ConsequenceTypeInsertionCalculator(genomeDBAdaptor); case DELETION: return new ConsequenceTypeDeletionCalculator(genomeDBAdaptor); case MNV: return new ConsequenceTypeMNVCalculator(genomeDBAdaptor); case CNV: if (variant.getSv().getCopyNumber() == null) { return new ConsequenceTypeGenericRegionCalculator(); } else if (variant.getSv().getCopyNumber() > 2) { return new ConsequenceTypeCNVGainCalculator(); } else { return new ConsequenceTypeDeletionCalculator(genomeDBAdaptor); } case DUPLICATION: return new ConsequenceTypeCNVGainCalculator(); case INVERSION: return new ConsequenceTypeGenericRegionCalculator(); case BREAKEND: return new ConsequenceTypeBNDCalculator(); default: throw new UnsupportedURLVariantFormat(); } }
mongoSv.put(SV_CISTART_FIELD, Arrays.asList(sv.getCiStartLeft(), sv.getCiStartRight())); mongoSv.put(SV_CIEND_FIELD, Arrays.asList(sv.getCiEndLeft(), sv.getCiEndRight())); if (sv.getCopyNumber() != null) { mongoSv.put(SV_CN_FIELD, sv.getCopyNumber());
ifNotNull(sv.getCiEndLeft(), svBuilder::setCiEndLeft); ifNotNull(sv.getCiEndRight(), svBuilder::setCiEndRight); ifNotNull(sv.getCopyNumber(), svBuilder::setCopyNumber); ifNotNull(sv.getRightSvInsSeq(), svBuilder::setRightSvInsSeq); ifNotNull(sv.getLeftSvInsSeq(), svBuilder::setLeftSvInsSeq);