code: public void run(List<Variant> variantList) {
          for (int i = 0; i < variantList.size(); i++) {
              Map<String, AdditionalAttribute> customAnnotation = getCustomAnnotation(variantList.get(i));
              // Update only if there are annotations for this variant. customAnnotation may be empty if the variant
              // exists in the vcf but the info field does not contain any of the required attributes
              if (customAnnotation != null && customAnnotation.get(fileId).getAttribute().size() > 0) {
                  VariantAnnotation variantAnnotation = variantList.get(i).getAnnotation();
                  if (variantAnnotation != null) {
                      Map<String, AdditionalAttribute> additionalAttributes = variantAnnotation.getAdditionalAttributes();
                      if (additionalAttributes == null) {
                          // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation
                          // at position i must correspond to variant i
                          variantAnnotation.setAdditionalAttributes(customAnnotation);
                      } else {
                          additionalAttributes.putAll(customAnnotation);
                          // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation
                          // at position i must correspond to variant i
  //                        variantAnnotation.setAdditionalAttributes(additionalAttributes);
                      }
                  }
              }
          }
      }
docs: Updates VariantAnnotation objects in variantAnnotationList.
  
  @param variantList List of Variant objects. variantList and variantAnnotationList must contain variants in the
  SAME order: variantAnnotation at position i must correspond to variant i