Examples of CramHeader

Examples of net.sf.cram.ReadWrite.CramHeader

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        baos.size() * 8f / baseCount);

    File cramFile = new File("c:/temp/test1.cram1");
    FileOutputStream fos = new FileOutputStream(cramFile);
    BufferedOutputStream bos = new BufferedOutputStream(fos);
    CramHeader cramHeader = new CramHeader(1, 0, bamFile.getName(),
        samFileReader.getFileHeader());

    ReadWrite.writeCramHeader(cramHeader, bos);
    ReadWrite.writeContainer(c, bos);
    bos.close();
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Examples of net.sf.cram.ReadWrite.CramHeader

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    BufferedInputStream bis = new BufferedInputStream(fis);

    SAMIterator iterator = new SAMIterator(bis,
        referenceSequenceFile);

    CramHeader cramHeader = iterator.getCramHeader();
    iterator.close();

    ProgressLogger progress = new ProgressLogger(log, 100000,
        "Validated Read");
    SamFileValidator v = new SamFileValidator(new PrintWriter(System.out),
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Examples of net.sf.cram.ReadWrite.CramHeader

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      }
    }

    long offset = 0;
    CountingInputStream cis = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(cis);
    offset = cis.getCount();

    SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    samFileWriterFactory.setAsyncOutputBufferSize(10000);
    samFileWriterFactory.setCreateIndex(false);
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Examples of net.sf.cram.ReadWrite.CramHeader

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    indexer = new CRAMIndexer(output, samFileHeader);
  }

  public BaiIndexer(InputStream is, File output) throws IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(this.is);
    samFileHeader = cramHeader.samFileHeader;

    indexer = new CRAMIndexer(output, samFileHeader);
  }
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Examples of net.sf.cram.ReadWrite.CramHeader

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  private CramIndex index;

  public CraiIndexer(InputStream is, File output)
      throws FileNotFoundException, IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(this.is);
    samFileHeader = cramHeader.samFileHeader;

    index = new CramIndex(new GZIPOutputStream(new BufferedOutputStream(
        new FileOutputStream(output))));
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Examples of net.sf.cram.ReadWrite.CramHeader

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      CipherOutputStream_256 cos = new CipherOutputStream_256(os, pass,
          128);
      os = cos.getCipherOutputStream();
    }

    CramHeader h = new CramHeader(2, 0, params.bamFile == null ? "STDIN"
        : params.bamFile.getName(), samFileReader.getFileHeader());
    long offset = ReadWrite.writeCramHeader(h, os);

    long bases = 0;
    long coreBytes = 0;
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Examples of net.sf.cram.ReadWrite.CramHeader

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        cramPath);

    if (stream == null)
      fail("CRAM file not found: " + cramPath);

    CramHeader cramHeader = ReadWrite.readCramHeader(stream);

    assertNotNull(cramHeader);
    assertEquals(cramHeader.majorVersion, 1) ;
    assertEquals(cramHeader.minorVersion, 1) ;
    assertNotNull(cramHeader.samFileHeader) ;
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Examples of net.sf.cram.ReadWrite.CramHeader

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      refBAOS.write(line.getBytes(), 0, line.length());
    }
    byte[] ref = refBAOS.toByteArray();
    refBAOS.close();

    CramHeader cramHeader = ReadWrite.readCramHeader(stream);
    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;
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