code: protected Pair<Integer, Integer> adjustedVariantStart(VariantProto.Variant variant,
                                                            List<VariantProto.AlternateCoordinate> secAlts,
                                                            Map<Integer, Character> referenceAlleles) {
          if (variant.getType().equals(VariantProto.VariantType.NO_VARIATION)) {
              return new ImmutablePair<>(variant.getStart(), variant.getEnd());
          }
          MutablePair<Integer, Integer> pos = adjustedVariantStart(variant.getStart(), variant.getEnd(), variant.getReference(), variant.getAlternate(), referenceAlleles, null);
  
          for (VariantProto.AlternateCoordinate alternateCoordinate: secAlts) {
              adjustedVariantStart(alternateCoordinate.getStart(), alternateCoordinate.getEnd(), alternateCoordinate.getReference(), alternateCoordinate.getAlternate(), referenceAlleles, pos);
          }
  
          return pos;
      }
docs: Adjust start/end if a reference base is required due to an empty allele. All variants are checked due to SecAlts.
  @param variant {@link VariantProto.Variant} object.
  @param referenceAlleles
  @return Pair<Integer, Integer> The adjusted (or same) start/end position e.g. SV and MNV as SecAlt, INDEL, etc.