Example #1
0
  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();
  }
Example #2
0
  /**
   * Read in a list of ExactCall objects from reader, keeping only those with starts in startsToKeep
   * or all sites (if this is empty)
   *
   * @param reader a just-opened reader sitting at the start of the file
   * @param startsToKeep a list of start position of the calls to keep, or empty if all calls should
   *     be kept
   * @param parser a genome loc parser to create genome locs
   * @return a list of ExactCall objects in reader
   * @throws IOException
   */
  public static List<ExactCall> readExactLog(
      final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser)
      throws IOException {
    if (reader == null) throw new IllegalArgumentException("reader cannot be null");
    if (startsToKeep == null) throw new IllegalArgumentException("startsToKeep cannot be null");
    if (parser == null) throw new IllegalArgumentException("GenomeLocParser cannot be null");

    List<ExactCall> calls = new LinkedList<ExactCall>();

    // skip the header line
    reader.readLine();

    // skip the first "type" line
    reader.readLine();

    while (true) {
      final VariantContextBuilder builder = new VariantContextBuilder();
      final List<Allele> alleles = new ArrayList<Allele>();
      final List<Genotype> genotypes = new ArrayList<Genotype>();
      final double[] posteriors = new double[2];
      final double[] priors = MathUtils.normalizeFromLog10(new double[] {0.5, 0.5}, true);
      final List<Integer> mle = new ArrayList<Integer>();
      final Map<Allele, Double> log10pNonRefByAllele = new HashMap<Allele, Double>();
      long runtimeNano = -1;

      GenomeLoc currentLoc = null;
      while (true) {
        final String line = reader.readLine();
        if (line == null) return calls;

        final String[] parts = line.split("\t");
        final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
        final String variable = parts[1];
        final String key = parts[2];
        final String value = parts[3];

        if (currentLoc == null) currentLoc = lineLoc;

        if (variable.equals("type")) {
          if (startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart())) {
            builder.alleles(alleles);
            final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
            builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
            builder.genotypes(genotypes);
            final int[] mleInts = ArrayUtils.toPrimitive(mle.toArray(new Integer[] {}));
            final AFCalcResult result =
                new AFCalcResult(mleInts, 1, alleles, posteriors, priors, log10pNonRefByAllele);
            calls.add(new ExactCall(builder.make(), runtimeNano, result));
          }
          break;
        } else if (variable.equals("allele")) {
          final boolean isRef = key.equals("0");
          alleles.add(Allele.create(value, isRef));
        } else if (variable.equals("PL")) {
          final GenotypeBuilder gb = new GenotypeBuilder(key);
          gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
          genotypes.add(gb.make());
        } else if (variable.equals("log10PosteriorOfAFEq0")) {
          posteriors[0] = Double.valueOf(value);
        } else if (variable.equals("log10PosteriorOfAFGt0")) {
          posteriors[1] = Double.valueOf(value);
        } else if (variable.equals("MLE")) {
          mle.add(Integer.valueOf(value));
        } else if (variable.equals("pNonRefByAllele")) {
          final Allele a = Allele.create(key);
          log10pNonRefByAllele.put(a, Double.valueOf(value));
        } else if (variable.equals("runtime.nano")) {
          runtimeNano = Long.valueOf(value);
        } else {
          // nothing to do
        }
      }
    }
  }