Examples of net.sf.cram.structure.Container

      records.add(record);
      baseCount += record.getReadLength();
    }


    long time1 = System.nanoTime();
    Container c = buildContainer(records, samFileHeader, true, 0, null,
        true);
    long time2 = System.nanoTime();
    System.out.println("Container written in " + (time2 - time1) / 1000000
        + " milli seconds");

      System.out.println(cramRecords.get(i).toString());


    System.out.println();


    long time1 = System.nanoTime();
    Container c = buildContainer(cramRecords,
        samFileReader.getFileHeader(), preserveReadNames, 0, null, true);
    long time2 = System.nanoTime();
    System.out.println("Container written in " + (time2 - time1) / 1000000
        + " milli seconds");

      it = si;
    } catch (IOException e) {
      throw new RuntimeEOFException(e);
    }


    Container c = null;
    for (int i = 0; i < filePointers.length; i += 2) {
      long containerOffset = filePointers[i] >>> 16;
      int sliceIndex = (int) ((filePointers[i] << 48) >>> 48);
      try {
        s.seek(containerOffset);

    assertNotNull(cramHeader);
    assertNotNull(cramHeader.samFileHeader);
    assertEquals(2, cramHeader.majorVersion);
    assertEquals(0, cramHeader.minorVersion);


    Container container = new Container();
    ContainerHeaderIO chio = new ContainerHeaderIO();
    chio.readContainerHeader(container, stream);
    assertNotNull(container);
    System.out.println(container);


    CompressionHeaderBLock chb = new CompressionHeaderBLock(stream);
    container.h = chb.getCompressionHeader();


    assertNotNull(container.h);
    System.out.println(container.h);


    SliceIO sio = new SliceIO();
    container.slices = new Slice[container.landmarks.length];
    for (int s = 0; s < container.landmarks.length; s++) {
      Slice slice = new Slice();
      sio.read(slice, stream);
      container.slices[s] = slice;
    }


    System.out.println(container);


    ArrayList<CramRecord> records = new ArrayList<CramRecord>(
        container.nofRecords);
    BLOCK_PROTO.getRecords(container.h, container,
        cramHeader.samFileHeader, records);
    
    testALignmentSpan(container, cramHeader, records);


    for (int i = 0; i < records.size(); i++) {
      if (i < 10)
        System.out.println(records.get(i).toString());
    }


    ExposedByteArrayOutputStream baos = new ExposedByteArrayOutputStream(
        BYTES);
    ReadWrite.writeCramHeader(cramHeader, baos);
    byte[] b = baos.toByteArray();
    ByteArrayInputStream bais = new ByteArrayInputStream(b);
    CramHeader cramHeader2 = ReadWrite.readCramHeader(bais);
    assertEquals(toString(cramHeader.samFileHeader),
        toString(cramHeader2.samFileHeader));


    BLOCK_PROTO.recordsPerSlice = container.slices[0].nofRecords;


    Container container2 = BLOCK_PROTO.buildContainer(records,
        cramHeader.samFileHeader, true, 0, container.h.substitutionMatrix, true);
    for (int i = 0; i < container.slices.length; i++) {
      container2.slices[i].refMD5 = container.slices[i].refMD5;
    }


    ReadWrite.writeContainer(container2, baos);


    bais = new ByteArrayInputStream(baos.toByteArray());


    cramHeader2 = ReadWrite.readCramHeader(bais);
    assertNotNull(cramHeader);
    assertNotNull(cramHeader.samFileHeader);
    assertEquals(2, cramHeader.majorVersion);
    assertEquals(0, cramHeader.minorVersion);


    Container container3 = new Container();
    chio.readContainerHeader(container3, bais);
    assertNotNull(container3);
    System.out.println(container3);


    CompressionHeaderBLock chb3 = new CompressionHeaderBLock(bais);

Examples of net.sf.cram.structure.Container

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