Exemplo n.º 1
0
  private Collection<VariantContext> getVariantContexts(
      RefMetaDataTracker tracker, ReferenceContext ref) {

    List<Feature> features = tracker.getValues(variants, ref.getLocus());
    List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());

    for (Feature record : features) {
      if (VariantContextAdaptors.canBeConvertedToVariantContext(record)) {
        // we need to special case the HapMap format because indels aren't handled correctly
        if (record instanceof RawHapMapFeature) {

          // is it an indel?
          RawHapMapFeature hapmap = (RawHapMapFeature) record;
          if (hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING)
              || hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING)) {
            // get the dbsnp object corresponding to this record (needed to help us distinguish
            // between insertions and deletions)
            VariantContext dbsnpVC = getDbsnp(hapmap.getName());
            if (dbsnpVC == null || dbsnpVC.isMixed()) continue;

            Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
            alleleMap.put(
                RawHapMapFeature.DELETION,
                Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
            alleleMap.put(
                RawHapMapFeature.INSERTION,
                Allele.create(
                    (char) ref.getBase() + ((RawHapMapFeature) record).getAlleles()[1],
                    !dbsnpVC.isSimpleInsertion()));
            hapmap.setActualAlleles(alleleMap);

            // also, use the correct positioning for insertions
            hapmap.updatePosition(dbsnpVC.getStart());

            if (hapmap.getStart() < ref.getWindow().getStart()) {
              logger.warn(
                  "Hapmap record at "
                      + ref.getLocus()
                      + " represents an indel too large to be converted; skipping...");
              continue;
            }
          }
        }

        // ok, we might actually be able to turn this record in a variant context
        VariantContext vc =
            VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);

        if (vc != null) // sometimes the track has odd stuff in it that can't be converted
        VCs.add(vc);
      }
    }

    return VCs;
  }
Exemplo n.º 2
0
  private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, GenomeLoc loc) {
    if (!wroteHeader) {
      wroteHeader = true;

      // setup the header fields
      Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
      hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
      hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));

      allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
      for (VCFHeaderLine field : hInfo) {
        if (field instanceof VCFFormatHeaderLine) {
          allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine) field).getID());
        }
      }

      samples = new LinkedHashSet<String>();
      if (sampleName != null) {
        samples.add(sampleName);
      } else {
        // try VCF first
        samples =
            SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));

        if (samples.isEmpty()) {
          List<Feature> features = tracker.getValues(variants, loc);
          if (features.size() == 0)
            throw new IllegalStateException(
                "No rod data is present, but we just created a VariantContext");

          Feature f = features.get(0);
          if (f instanceof RawHapMapFeature)
            samples.addAll(Arrays.asList(((RawHapMapFeature) f).getSampleIDs()));
          else samples.addAll(vc.getSampleNames());
        }
      }

      vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
    }

    vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
    vcfwriter.add(vc);
  }