Esempio n. 1
0
  private boolean isConcordant(VariantContext vc, Collection<VariantContext> compVCs) {
    if (vc == null || compVCs == null || compVCs.isEmpty()) return false;

    // if we're not looking for specific samples then the fact that we have both VCs is enough to
    // call it concordant.
    if (NO_SAMPLES_SPECIFIED) return true;

    // make a list of all samples contained in this variant VC that are being tracked by the user
    // command line arguments.
    Set<String> variantSamples = vc.getSampleNames();
    variantSamples.retainAll(samples);

    // check if we can find all samples from the variant rod in the comp rod.
    for (String sample : variantSamples) {
      boolean foundSample = false;
      for (VariantContext compVC : compVCs) {
        Genotype varG = vc.getGenotype(sample);
        Genotype compG = compVC.getGenotype(sample);
        if (haveSameGenotypes(varG, compG)) {
          foundSample = true;
          break;
        }
      }
      // if at least one sample doesn't have the same genotype, we don't have concordance
      if (!foundSample) {
        return false;
      }
    }
    return true;
  }
  /**
   * Compares the covariate report lists.
   *
   * @param diffs map where to annotate the difference.
   * @param other the argument collection to compare against.
   * @param thisRole the name for this argument collection that makes sense to the user.
   * @param otherRole the name for the other argument collection that makes sense to the end user.
   * @return <code>true</code> if a difference was found.
   */
  @Requires("diffs != null && other != null && thisRole != null && otherRole != null")
  private boolean compareRequestedCovariates(
      final Map<String, String> diffs,
      final RecalibrationArgumentCollection other,
      final String thisRole,
      final String otherRole) {

    final Set<String> beforeNames = new HashSet<>(this.COVARIATES.length);
    final Set<String> afterNames = new HashSet<>(other.COVARIATES.length);
    Utils.addAll(beforeNames, this.COVARIATES);
    Utils.addAll(afterNames, other.COVARIATES);
    final Set<String> intersect = new HashSet<>(Math.min(beforeNames.size(), afterNames.size()));
    intersect.addAll(beforeNames);
    intersect.retainAll(afterNames);

    String diffMessage = null;
    if (intersect.size()
        == 0) { // In practice this is not possible due to required covariates but...
      diffMessage =
          String.format(
              "There are no common covariates between '%s' and '%s'"
                  + " recalibrator reports. Covariates in '%s': {%s}. Covariates in '%s': {%s}.",
              thisRole,
              otherRole,
              thisRole,
              Utils.join(", ", this.COVARIATES),
              otherRole,
              Utils.join(",", other.COVARIATES));
    } else if (intersect.size() != beforeNames.size() || intersect.size() != afterNames.size()) {
      beforeNames.removeAll(intersect);
      afterNames.removeAll(intersect);
      diffMessage =
          String.format(
              "There are differences in the set of covariates requested in the"
                  + " '%s' and '%s' recalibrator reports. "
                  + " Exclusive to '%s': {%s}. Exclusive to '%s': {%s}.",
              thisRole,
              otherRole,
              thisRole,
              Utils.join(", ", beforeNames),
              otherRole,
              Utils.join(", ", afterNames));
    }
    if (diffMessage != null) {
      diffs.put("covariate", diffMessage);
      return true;
    } else {
      return false;
    }
  }