Exemplo n.º 1
0
  /** attempt to close the VCF file */
  public void close() {
    // try to close the vcf stream
    try {
      mWriter.flush();
      mWriter.close();
    } catch (IOException e) {
      throw new TribbleException(
          "Unable to close " + locationString() + " because of " + e.getMessage());
    }

    // try to close the index stream (keep it separate to help debugging efforts)
    if (indexer != null) {
      try {
        Index index = indexer.finalizeIndex(positionalStream.getPosition());
        index.write(idxStream);
        idxStream.close();
      } catch (IOException e) {
        throw new TribbleException(
            "Unable to close index for " + locationString() + " because of " + e.getMessage());
      }
    }
  }
Exemplo n.º 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());
    }
  }