Exemplo n.º 1
0
  /**
   * Function that process a set of statuses into strings
   *
   * @param statuses the set of statuses to be converted
   * @return a matching set of strings
   */
  private List<String> statusToStrings(
      Iterable<CallableStatus> statuses, final boolean isInfoField) {
    List<String> output = new LinkedList<>();

    for (CallableStatus status : statuses)
      if (isInfoField || status != CallableStatus.PASS) output.add(status.name());

    return output;
  }
Exemplo n.º 2
0
  /**
   * Gets the header lines for the VCF writer
   *
   * @return A set of VCF header lines
   */
  private static Set<VCFHeaderLine> getHeaderInfo() {
    Set<VCFHeaderLine> headerLines = new HashSet<>();

    // INFO fields for overall data
    headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AVG_INTERVAL_DP_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY));
    headerLines.add(
        new VCFInfoHeaderLine(
            "Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));

    // FORMAT fields for each genotype
    headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
    headerLines.add(
        GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY));
    headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.LOW_COVERAGE_LOCI));
    headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ZERO_COVERAGE_LOCI));

    // FILTER fields
    for (CallableStatus stat : CallableStatus.values())
      headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description));

    return headerLines;
  }