code: public static AlternateCoordinate getMainAlternate(Variant variant) {
          VariantType type;
          switch (variant.getType()) {
              case SNP:
                  type = VariantType.SNV;
                  break;
              case MNP:
                  type = VariantType.MNV;
                  break;
              case SV:
                  type = VariantBuilder.inferType(variant.getReference(), variant.getAlternate());
                  break;
              default:
                  type = variant.getType();
  
          }
          return new AlternateCoordinate(variant.getChromosome(), variant.getStart(), variant.getEnd(),
                  variant.getReference(), variant.getAlternate(), type);
      }
docs: Get the variant as Alternate Coordinate.
  
  At this point, we don't care if the Alternate is SNP or SNV.
  In case that the variant is SV, recalculate the type, just in case the size has changed.
  
  @param variant Variant
  @return Variant as AlternateCoordinate