ifNotNull(sv.getCiStartLeft(), svBuilder::setCiStartLeft); ifNotNull(sv.getCiStartRight(), svBuilder::setCiStartRight); 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); ifNotNull(sv.getType(), type -> svBuilder.setType(VariantProto.StructuralVariantType.valueOf(sv.getType().toString()))); if (sv.getBreakend() != null) { Breakend bnd = sv.getBreakend(); VariantProto.Breakend.Builder bndBuilder = VariantProto.Breakend.newBuilder(); ifNotNull(bnd.getInsSeq(), bndBuilder::setInsSeq); ifNotNull(bnd.getMate().getChromosome(), bndMateBuilder::setChromosome); ifNotNull(bnd.getMate().getPosition(), bndMateBuilder::setPosition); ifNotNull(bnd.getMate().getCiPositionLeft(), bndMateBuilder::setCiPositionLeft); ifNotNull(bnd.getMate().getCiPositionRight(), bndMateBuilder::setCiPositionRight); bndBuilder.setMate(bndMateBuilder); ifNotNull(bnd.getOrientation(), type -> bndBuilder.setOrientation(VariantProto.BreakendOrientation.valueOf(type.toString())));