Class VcfRecordMerger

src/main/java/com/rtg/vcf/VcfRecordMerger.java:51–395

Provides routines for merging VCF records.

 * Provides routines for merging VCF records.
 */
public class VcfRecordMerger {

  /** Maximum number of duplicate warnings to explicitly print. */
  public static final long DUPLICATE_WARNINGS_TO_PRINT = 5;

  private long mMultipleRecordsForSampleCount = 0;
  private String mDefaultFormat = VcfUtils.FORMAT_GENOTYPE;
  private boolean mAllowRecordMerging = true;
  private boolean mPaddingAware = true;
  private boolean mDropUnmergeable;
  private VcfHeader mHeader;
  private Set<String> mUnmergeableFormatFields = Collections.emptySet();
  private Set<String> mUnmergeableInfoFields = Collections.emptySet();


  /**
   * @param defaultFormat the ID of the FORMAT field to fall back to when merging sample-free VCFs with those containing samples
   * @return this object, for call chaining
   */
  public final VcfRecordMerger setDefaultFormat(String defaultFormat) {
    mDefaultFormat = defaultFormat;
    return this;
  }

  /**
   * Sets whether we can attempt to merge multiple records at the same position (e.g. multiple samples).
   * Note that other options may subsequent veto a multi-record merge in specific conditions.
   *
   * @param recordMerging if false, records at the same position will never be combined into a single record.
   * @return this object, for call chaining
   */
  public final VcfRecordMerger setAllowMerging(boolean recordMerging) {
    mAllowRecordMerging = recordMerging;
    return this;
  }

  /**
   * Sets the behaviour when merging records containing padding bases with those without padding bases,
   * to avoid semantic pollution of annotations.
   *
   * @param paddingAware if true, do not merge records containing padding bases with those without padding bases,
   * if false, allow merging to proceed.
   * @return this object, for call chaining
   */
  public final VcfRecordMerger setPaddingAware(boolean paddingAware) {
    mPaddingAware = paddingAware;
    return this;
  }

  /**
   * Sets the behaviour when encountering any non-mergeable FORMAT fields or duplicate records for the same sample.
   *
   * @param dropUnmergeable if false, non-mergeable fields will prevent merging. If true, non-mergeable fields
   * will be dropped so the merge can continue.
   * @return this object, for call chaining
   */
  public VcfRecordMerger setDropUnmergeable(boolean dropUnmergeable) {
    mDropUnmergeable = dropUnmergeable;