protected final void printCallInfo(
      final VariantContext vc,
      final double[] log10AlleleFrequencyPriors,
      final long runtimeNano,
      final AFCalcResult result) {
    printCallElement(vc, "type", "ignore", vc.getType());

    int allelei = 0;
    for (final Allele a : vc.getAlleles())
      printCallElement(vc, "allele", allelei++, a.getDisplayString());

    for (final Genotype g : vc.getGenotypes())
      printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());

    for (int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++)
      printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);

    printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
    printCallElement(vc, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
    printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());

    for (final Allele allele : result.getAllelesUsedInGenotyping()) {
      if (allele.isNonReference()) {
        printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
        printCallElement(
            vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
      }
    }

    callReport.flush();
  }
Exemple #2
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  static boolean someSampleHasDoubleNonReferenceAllele(VariantContext vc1, VariantContext vc2) {
    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(); // this is OK, since allSamplesAreMergeable()

        if (all1.isNonReference() && all2.isNonReference()) // corresponding alleles are alternate
        return true;
      }
    }

    return false;
  }