Examples of net.sf.cram.io.ExposedByteArrayOutputStream.toByteArray()

Class net.sf.cram.io.ExposedByteArrayOutputStream

Examples of net.sf.cram.io.ExposedByteArrayOutputStream.toByteArray()

net.sf.cram.io.ExposedByteArrayOutputStream.toByteArray()

      headerOS.write(headerBodyOS.getBuffer(), 0, headerBodyOS.size());
    } catch (IOException e) {
      throw new RuntimeException(e);
    }


    return headerOS.toByteArray();
  }


  private static long writeContainer(SAMFileHeader samFileHeader,
      OutputStream os) throws IOException {
    Block block = new Block();

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        : BlockContentType.RESERVED;


    bos.close();
    slice.coreBlock = new Block();
    slice.coreBlock.method = BlockCompressionMethod.RAW.ordinal();
    slice.coreBlock.setRawContent(bitBAOS.toByteArray());
    slice.coreBlock.contentType = BlockContentType.CORE;


    slice.external = new HashMap<Integer, Block>();
    for (Integer i : map.keySet()) {
      ExposedByteArrayOutputStream os = map.get(i);

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      Block externalBlock = new Block();
      externalBlock.contentType = BlockContentType.EXTERNAL;
      externalBlock.method = BlockCompressionMethod.GZIP.ordinal();
      externalBlock.contentId = i;


      externalBlock.setRawContent(os.toByteArray());
      slice.external.put(i, externalBlock);
    }


    return slice;
  }

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    }


    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));

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      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);

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