Method adjust

src/main/java/com/rtg/vcf/Adjuster.java:161–183

Potentially change, delete, or insert VCF FORMAT and INFO fields in accordance with a change of alleles from the original record to the replacement. For example, if alleles have been combined, then it is appropriate to add the AD elements for the corresponding alleles. @param original original VCF

(final VcfRecord original, final VcfRecord replacement, final int[] alleleMap)

   * @param alleleMap mapping from alleles in original record into replacement record
   */
  public void adjust(final VcfRecord original, final VcfRecord replacement, final int[] alleleMap) {
    try {
      final int numAlleles = MathUtils.max(alleleMap) + 1;
      assert numAlleles == replacement.getAltCalls().size() + 1;

      for (String field : original.getInfo().keySet()) {
        if (mInfoPolicies.containsKey(field)) {
          adjustInfoField(original, replacement, alleleMap, numAlleles, field, mInfoPolicies.get(field));
        }
      }
      for (String field : original.getFormats()) {
        if (mFormatPolicies.containsKey(field)) {
          adjustFormatField(original, replacement, alleleMap, numAlleles, field, mFormatPolicies.get(field));
        }
      }
    } catch (final VcfFormatException e) {
      throw e;
    } catch (final RuntimeException e) {
      // Log any records that lead to exceptions during adjustment
      Diagnostic.userLog("Problem adjusting: " + original.toString());
      throw e;
    }
  }

  private void validateTypedField(TypedField<?> f) {
    final VcfNumber n = f.getNumber();