Class Variant

src/main/java/com/rtg/vcf/eval/Variant.java:50–317

Holds information about a single variant that has not yet been oriented in a haplotype. A Variant can be asked for alleles using original GT-style allele IDs, including -1 for missing value.

 * A Variant can be asked for alleles using original GT-style allele IDs, including -1 for missing value.
 */
public class Variant implements Comparable<Variant>, VariantId {

  static final SequenceNameLocusComparator NATURAL_COMPARATOR = new SequenceNameLocusComparator();
  static final Comparator<VariantId> ID_COMPARATOR = new Comparator<VariantId>() {
    @Override
    public int compare(VariantId o1, VariantId o2) {
      return Integer.compare(o1.getId(), o2.getId());
    }
  };

  private SequenceNameLocus mLocus;
  private final int mId;
  private final Allele[] mAlleles;
  private final boolean mPhased;
  private byte mStatus = 0;

  /**
   * Construct the variant
   * @param id the ID of the variant when read from the original input
   * @param seq chromosome name
   * @param alleles array of alleles where each entry corresponds to the allele for GT ID + 1
   * @param phased true if the variant call was phased
   */
  public Variant(int id, String seq, Allele[] alleles, boolean phased) {
    this(id, seq, Allele.getAlleleBounds(alleles), alleles, phased);
  }

  /**
   * Construct the variant
   * @param id the ID of the variant when read from the original input
   * @param seq chromosome name
   * @param bounds bounds of the alleles
   * @param alleles array of alleles where each entry corresponds to the allele for GT ID + 1
   * @param phased true if the variant call was phased
   */
  private Variant(int id, String seq, Range bounds, Allele[] alleles, boolean phased) {
    //super(seq, bounds.getStart(), bounds.getEnd());
    mLocus = new SequenceNameLocusSimple(seq, bounds.getStart(), bounds.getEnd());
    mId = id;
    mPhased = phased;
    mAlleles = alleles;
  }

  void trimAlleles() {
    trimAlleles(true);
  }

  void trimAlleles(boolean leftFirst) {
    // Element 0 is missing value token
    final byte[] ref = mAlleles[1].nt();
    mAlleles[1] = null;
    for (int i = 2; i < mAlleles.length; i++) {
      final Allele a = mAlleles[i];
      if (a != null && !a.unknown()) {
        final byte[] alt = a.nt();
        final int stripLeading;
        final int stripTrailing;
        if (leftFirst) {