Examples of net.sf.cram.structure.CompressionHeader

  private static Log log = Log.getInstance(CompressionHeaderFactory.class);
  private static final int oqz = ReadTag.nameType3BytesToInt("OQ", 'Z');
  private static final int bqz = ReadTag.nameType3BytesToInt("OQ", 'Z');


  public CompressionHeader build(List<CramRecord> records, SubstitutionMatrix substitutionMatrix) {
    CompressionHeader h = new CompressionHeader();
    h.externalIds = new ArrayList<Integer>();
    int exCounter = 0;


    int baseID = exCounter++;
    h.externalIds.add(baseID);

      long globalRecordCounter, SubstitutionMatrix substitutionMatrix,
      boolean AP_delta) throws IllegalArgumentException,
      IllegalAccessException, IOException {
    // get stats, create compression header and slices
    long time1 = System.nanoTime();
    CompressionHeader h = new CompressionHeaderFactory().build(records,
        substitutionMatrix);
    h.AP_seriesDelta = AP_delta;
    long time2 = System.nanoTime();


    h.readNamesIncluded = preserveReadNames;

Related Classes of net.sf.cram.structure.CompressionHeader

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