Exemple #1
0
  /** Uncompress VCF entry having genotypes in "HO,HE,NA" fields */
  public VcfEntry uncompressGenotypes() {
    // Not compressed? Nothing to do
    if (!isCompressedGenotypes()) return this;

    // Get 'sparse' matrix entries
    String hoStr = getInfo(VCF_INFO_HOMS);
    String heStr = getInfo(VCF_INFO_HETS);
    String naStr = getInfo(VCF_INFO_NAS);

    // Parse 'sparse' entries
    List<String> sampleNames = getVcfFileIterator().getVcfHeader().getSampleNames();
    if (sampleNames == null)
      throw new RuntimeException(
          "Cannot find sample names in VCF header. Unable to uncompress genotypes.");
    int numSamples = sampleNames.size();
    byte gt[] = new byte[numSamples];
    parseSparseGt(naStr, gt, -1);
    parseSparseGt(heStr, gt, 1);
    parseSparseGt(hoStr, gt, 2);

    // Remove info fields
    if (hoStr != null) rmInfo(VCF_INFO_HOMS);
    if (heStr != null) rmInfo(VCF_INFO_HETS);
    if (naStr != null) rmInfo(VCF_INFO_NAS);
    setFormat("GT");

    // Create output string
    for (int i = 0; i < gt.length; i++) {
      String gtStr;
      switch (gt[i]) {
        case -1:
          gtStr = "./.";
          break;

        case 0:
          gtStr = "0/0";
          break;

        case 1:
          gtStr = "0/1";
          break;

        case 2:
          gtStr = "1/1";
          break;

        default:
          throw new RuntimeException("Unknown code '" + gt[i] + "'");
      }

      addGenotype(gtStr);
    }

    return this;
  }
Exemple #2
0
  /** Parse GENOTPYE entries */
  void parseGenotypes() {
    if (isCompressedGenotypes()) {
      uncompressGenotypes();
    } else {
      vcfGenotypes = new ArrayList<>();

      // No genotype string? => Nothing to do
      if (genotypeFieldsStr == null) return;

      // Split genotypes and parse them
      genotypeFields = genotypeFieldsStr.split("\t");
      for (int i = 0; i < genotypeFields.length; i++) {
        String gen = genotypeFields[i];
        if (gen.equals(VcfFileIterator.MISSING)) gen = "";
        addGenotype(gen);
      }
    }
  }