Exemplo n.º 1
0
  /** Add some lines to header before showing it */
  @Override
  public boolean addHeaders(VcfFileIterator vcfFile) {
    super.addHeaders(vcfFile);
    for (String key : fieldsToAdd.keySet()) {
      // Get type
      String type = fieldsType.get(key);
      if (type == null) {
        System.err.println("WARNING: Cannot find type for field '" + key + "', using 'String'.");
        type = VcfInfoType.String.toString();
      }

      String infoKey = VcfEntry.vcfInfoKeySafe(DBNSFP_VCF_INFO_PREFIX + key);
      vcfFile
          .getVcfHeader()
          .addLine(
              "##INFO=<ID="
                  + infoKey
                  + ",Number=A,Type="
                  + type
                  + ",Description=\""
                  + fieldsToAdd.get(key)
                  + "\">");
    }

    return false;
  }
Exemplo n.º 2
0
  /** Annotate a VCF file using dbNSFP */
  ArrayList<VcfEntry> annotate(boolean createList) {
    ArrayList<VcfEntry> list = (createList ? new ArrayList<VcfEntry>() : null);

    // Open VCF file
    vcfFile = new VcfFileIterator(vcfFileName);
    vcfFile.setDebug(debug);

    // Initialize annotations
    try {
      annotateInit(vcfFile);
    } catch (Exception e) {
      throw new RuntimeException(e);
    }

    // Annotate VCF file
    if (verbose) Timer.showStdErr("Annotating file '" + vcfFileName + "'");
    boolean showHeader = true;
    int pos = -1;
    String chr = "";
    for (VcfEntry vcfEntry : vcfFile) {
      try {
        // Show header?
        if (showHeader) {
          // Add VCF header
          addHeaders(vcfFile);
          String headerStr = vcfFile.getVcfHeader().toString();
          if (!headerStr.isEmpty()) print(headerStr);
          showHeader = false;

          // Check that the fields we want to add are actually in the database
          checkFieldsToAdd();
        }

        // Check if file is sorted
        if (vcfEntry.getChromosomeName().equals(chr) && vcfEntry.getStart() < pos) {
          fatalError(
              "Your VCF file should be sorted!" //
                  + "\n\tPrevious entry "
                  + chr
                  + ":"
                  + pos //
                  + "\n\tCurrent entry  "
                  + vcfEntry.getChromosomeName()
                  + ":"
                  + (vcfEntry.getStart() + 1) //
              );
        }

        // Annotate
        annotate(vcfEntry);

        // Show
        print(vcfEntry);
        if (list != null) list.add(vcfEntry);
        count++;

        // Update chr:pos
        chr = vcfEntry.getChromosomeName();
        pos = vcfEntry.getStart();
      } catch (IOException e) {
        throw new RuntimeException(e);
      }
    }

    annotateFinish();
    vcfFile.close();

    // Show some stats
    if (verbose) {
      double perc = (100.0 * countAnnotated) / count;
      Timer.showStdErr(
          "Done." //
              + "\n\tTotal annotated entries : "
              + countAnnotated //
              + "\n\tTotal entries           : "
              + count //
              + "\n\tPercent                 : "
              + String.format("%.2f%%", perc) //
          );
    }

    return list;
  }