Esempio n. 1
0
  /**
   * Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN,
   * AC, AF).
   *
   * @param vc the VariantContext record to subset
   * @param samples the samples to extract
   * @return the subsetted VariantContext
   */
  private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
    if (samples == null || samples.isEmpty()) return vc;

    ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
    for (Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet()) {
      if (samples.contains(genotypePair.getKey())) genotypes.add(genotypePair.getValue());
    }

    VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());

    // if we have fewer alternate alleles in the selected VC than in the original VC, we need to
    // strip out the GL/PLs (because they are no longer accurate)
    if (vc.getAlleles().size() != sub.getAlleles().size())
      sub = VariantContext.modifyGenotypes(sub, VariantContextUtils.stripPLs(vc.getGenotypes()));

    HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());

    int depth = 0;
    for (String sample : sub.getSampleNames()) {
      Genotype g = sub.getGenotype(sample);

      if (g.isNotFiltered() && g.isCalled()) {

        String dp = (String) g.getAttribute("DP");
        if (dp != null
            && !dp.equals(VCFConstants.MISSING_DEPTH_v3)
            && !dp.equals(VCFConstants.MISSING_VALUE_v4)) {
          depth += Integer.valueOf(dp);
        }
      }
    }

    if (KEEP_ORIGINAL_CHR_COUNTS) {
      if (attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY))
        attributes.put("AC_Orig", attributes.get(VCFConstants.ALLELE_COUNT_KEY));
      if (attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
        attributes.put("AF_Orig", attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY));
      if (attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY))
        attributes.put("AN_Orig", attributes.get(VCFConstants.ALLELE_NUMBER_KEY));
    }

    VariantContextUtils.calculateChromosomeCounts(sub, attributes, false);
    attributes.put("DP", depth);

    sub = VariantContext.modifyAttributes(sub, attributes);

    return sub;
  }
Esempio n. 2
0
  /**
   * add a record to the file
   *
   * @param vc the Variant Context object
   * @param refBase the ref base used for indels
   * @param refBaseShouldBeAppliedToEndOfAlleles *** THIS SHOULD BE FALSE EXCEPT FOR AN INDEL AT THE
   *     EXTREME BEGINNING OF A CONTIG (WHERE THERE IS NO PREVIOUS BASE, SO WE USE THE BASE AFTER
   *     THE EVENT INSTEAD)
   */
  public void add(VariantContext vc, byte refBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
    if (mHeader == null)
      throw new IllegalStateException(
          "The VCF Header must be written before records can be added: " + locationString());

    if (doNotWriteGenotypes) vc = VariantContext.modifyGenotypes(vc, null);

    try {
      vc =
          VariantContext.createVariantContextWithPaddedAlleles(
              vc, refBase, refBaseShouldBeAppliedToEndOfAlleles);

      // if we are doing on the fly indexing, add the record ***before*** we write any bytes
      if (indexer != null) indexer.addFeature(vc, positionalStream.getPosition());

      Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size());
      alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup

      // CHROM
      mWriter.write(vc.getChr());
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // POS
      mWriter.write(String.valueOf(vc.getStart()));
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // ID
      String ID = vc.hasID() ? vc.getID() : VCFConstants.EMPTY_ID_FIELD;
      mWriter.write(ID);
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // REF
      alleleMap.put(vc.getReference(), "0");
      String refString = vc.getReference().getDisplayString();
      mWriter.write(refString);
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // ALT
      if (vc.isVariant()) {
        Allele altAllele = vc.getAlternateAllele(0);
        alleleMap.put(altAllele, "1");
        String alt = altAllele.getDisplayString();
        mWriter.write(alt);

        for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
          altAllele = vc.getAlternateAllele(i);
          alleleMap.put(altAllele, String.valueOf(i + 1));
          alt = altAllele.getDisplayString();
          mWriter.write(",");
          mWriter.write(alt);
        }
      } else {
        mWriter.write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
      }
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // QUAL
      if (!vc.hasNegLog10PError()) mWriter.write(VCFConstants.MISSING_VALUE_v4);
      else mWriter.write(getQualValue(vc.getPhredScaledQual()));
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // FILTER
      String filters =
          vc.isFiltered()
              ? ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters()))
              : (filtersWereAppliedToContext || vc.filtersWereApplied()
                  ? VCFConstants.PASSES_FILTERS_v4
                  : VCFConstants.UNFILTERED);
      mWriter.write(filters);
      mWriter.write(VCFConstants.FIELD_SEPARATOR);

      // INFO
      Map<String, String> infoFields = new TreeMap<String, String>();
      for (Map.Entry<String, Object> field : vc.getAttributes().entrySet()) {
        String key = field.getKey();
        if (key.equals(VariantContext.ID_KEY)
            || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)
            || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY)
            || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY)) continue;

        String outputValue = formatVCFField(field.getValue());
        if (outputValue != null) infoFields.put(key, outputValue);
      }
      writeInfoString(infoFields);

      // FORMAT
      if (vc.hasAttribute(VariantContext.UNPARSED_GENOTYPE_MAP_KEY)) {
        mWriter.write(VCFConstants.FIELD_SEPARATOR);
        mWriter.write(vc.getAttributeAsString(VariantContext.UNPARSED_GENOTYPE_MAP_KEY, ""));
      } else {
        List<String> genotypeAttributeKeys = new ArrayList<String>();
        if (vc.hasGenotypes()) {
          genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc));
        } else if (mHeader.hasGenotypingData()) {
          // this needs to be done in case all samples are no-calls
          genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
        }

        if (genotypeAttributeKeys.size() > 0) {
          String genotypeFormatString =
              ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
          mWriter.write(VCFConstants.FIELD_SEPARATOR);
          mWriter.write(genotypeFormatString);

          addGenotypeData(vc, alleleMap, genotypeAttributeKeys);
        }
      }

      mWriter.write("\n");
      mWriter.flush(); // necessary so that writing to an output stream will work
    } catch (IOException e) {
      throw new RuntimeException("Unable to write the VCF object to " + locationString());
    }
  }