code: public List<AlternateCoordinate> buildAltList(Variant variant) {
          AlternateCoordinate mainAlternate = getMainAlternate(variant);
          List<AlternateCoordinate> alternates = new ArrayList<>();
          boolean emptyRefBlock = mainAlternate.getType().equals(VariantType.NO_VARIATION)
                  && (mainAlternate.getAlternate().isEmpty() || mainAlternate.getAlternate().equals(Allele.NO_CALL_STRING));
          // Skip Reference Blocks (NO_VARIATION) where the alternate is empty
          if (!emptyRefBlock) {
              alternates.add(mainAlternate);
          }
          StudyEntry se = getStudy(variant);
          if(se.getSecondaryAlternates() != null){
              se.getSecondaryAlternates().forEach( alt -> alternates.add(copyAlt(variant, alt)));
          }
          return alternates;
      }
docs: Build a list of all the alternates from a variant. Includes the main and the secondary alternates.
  @param variant
  @return