Examples of net.sf.cram.index.CramIndex.Entry


  @Test
  public void test() throws IOException, CloneNotSupportedException {
    List<CramIndex.Entry> list = new ArrayList<CramIndex.Entry>();


    Entry e = new Entry();
    e.sequenceId = 1;
    e.alignmentStart = 1;
    e.containerStartOffset = 1;
    e.sliceOffset = 1;
    e.sliceSize = 0;
    list.add(e);


    e = e.clone();
    e.alignmentStart = 2;
    e.containerStartOffset = 2;
    e.sliceOffset = 1;
    e.sliceSize = 0;
    list.add(e);


    e = e.clone();
    e.alignmentStart = 3;
    e.containerStartOffset = 3;
    e.sliceOffset = 1;
    e.sliceSize = 0;
    list.add(e);

    { // try crai:
      List<CramIndex.Entry> entries = getCraiEntries(cramFile,
          cramHeader, cramFileInputStream, location);
      if (entries != null) {
        try {
          Entry leftmost = CramIndex.getLeftmost(entries);
          cramFileInputStream.seek(leftmost.containerStartOffset);
          c = ReadWrite.readContainerHeader(cramFileInputStream);
          if (c == null) return null ;
          if (c.alignmentStart + c.alignmentSpan > location.start) {
            cramFileInputStream.seek(leftmost.containerStartOffset);

Related Classes of net.sf.cram.index.CramIndex.Entry

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