예제 #1
0
  public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
    if (tracker == null || !BaseUtils.isRegularBase(ref.getBase())) return 0;

    Collection<VariantContext> contexts = getVariantContexts(tracker, ref);

    for (VariantContext vc : contexts) {
      VariantContextBuilder builder = new VariantContextBuilder(vc);

      // set the appropriate sample name if necessary
      if (sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName())) {
        Genotype g =
            new GenotypeBuilder(vc.getGenotype(variants.getName())).name(sampleName).make();
        builder.genotypes(g);
      }

      final VariantContext withID = variantOverlapAnnotator.annotateRsID(tracker, builder.make());
      writeRecord(withID, tracker, ref.getLocus());
    }

    return 1;
  }
예제 #2
0
  /**
   * Takes the interval, finds it in the stash, prints it to the VCF
   *
   * @param stats The statistics of the interval
   * @param refAllele the reference allele
   */
  private void outputStatsToVCF(final IntervalStratification stats, final Allele refAllele) {
    GenomeLoc interval = stats.getInterval();

    final List<Allele> alleles = new ArrayList<>();
    final Map<String, Object> attributes = new HashMap<>();
    final ArrayList<Genotype> genotypes = new ArrayList<>();

    for (String sample : samples) {
      final GenotypeBuilder gb = new GenotypeBuilder(sample);

      SampleStratification sampleStat = stats.getSampleStatistics(sample);
      gb.attribute(
          GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY,
          sampleStat.averageCoverage(interval.size()));
      gb.attribute(GATKVCFConstants.LOW_COVERAGE_LOCI, sampleStat.getNLowCoveredLoci());
      gb.attribute(GATKVCFConstants.ZERO_COVERAGE_LOCI, sampleStat.getNUncoveredLoci());
      gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));

      genotypes.add(gb.make());
    }
    alleles.add(refAllele);
    alleles.add(SYMBOLIC_ALLELE);
    VariantContextBuilder vcb =
        new VariantContextBuilder(
            "DiagnoseTargets",
            interval.getContig(),
            interval.getStart(),
            interval.getStop(),
            alleles);

    vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR);
    vcb.filters(new LinkedHashSet<>(statusToStrings(stats.callableStatuses(), true)));

    attributes.put(VCFConstants.END_KEY, interval.getStop());
    attributes.put(GATKVCFConstants.AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size()));
    attributes.put(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY, stats.gcContent());

    vcb = vcb.attributes(attributes);
    vcb = vcb.genotypes(genotypes);

    vcfWriter.add(vcb.make());
  }