Exemplo n.º 1
0
  static boolean doubleAllelesSegregatePerfectlyAmongSamples(
      VariantContext vc1, VariantContext vc2) {
    // Check that Alleles at vc1 and at vc2 always segregate together in all samples (including
    // reference):
    Map<Allele, Allele> allele1ToAllele2 = new HashMap<Allele, Allele>();
    Map<Allele, Allele> allele2ToAllele1 = new HashMap<Allele, Allele>();

    // Note the segregation of the alleles for the reference genome:
    allele1ToAllele2.put(vc1.getReference(), vc2.getReference());
    allele2ToAllele1.put(vc2.getReference(), vc1.getReference());

    // Note the segregation of the alleles for each sample (and check that it is consistent with the
    // reference and all previous samples).
    for (final Genotype gt1 : vc1.getGenotypes()) {
      Genotype gt2 = vc2.getGenotype(gt1.getSampleName());

      List<Allele> site1Alleles = gt1.getAlleles();
      List<Allele> site2Alleles = gt2.getAlleles();

      Iterator<Allele> all2It = site2Alleles.iterator();
      for (Allele all1 : site1Alleles) {
        Allele all2 = all2It.next();

        Allele all1To2 = allele1ToAllele2.get(all1);
        if (all1To2 == null) allele1ToAllele2.put(all1, all2);
        else if (!all1To2.equals(all2)) // all1 segregates with two different alleles at site 2
        return false;

        Allele all2To1 = allele2ToAllele1.get(all2);
        if (all2To1 == null) allele2ToAllele1.put(all2, all1);
        else if (!all2To1.equals(all1)) // all2 segregates with two different alleles at site 1
        return false;
      }
    }

    return true;
  }
  @Requires({"eval != null", "comp != null"})
  private EvalCompMatchType doEvalAndCompMatch(
      final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) {
    // find all of the matching comps
    if (comp.getType() != eval.getType()) return EvalCompMatchType.NO_MATCH;

    // find the comp which matches both the reference allele and alternate allele from eval
    final Allele altEval =
        eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
    final Allele altComp =
        comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
    if ((altEval == null && altComp == null)
        || (altEval != null
            && altEval.equals(altComp)
            && eval.getReference().equals(comp.getReference()))) return EvalCompMatchType.STRICT;
    else return requireStrictAlleleMatch ? EvalCompMatchType.NO_MATCH : EvalCompMatchType.LENIENT;
  }