Package htsjdk.samtools.cram.build

Class CramIO

java.lang.Object
htsjdk.samtools.cram.build.CramIO
public final class CramIO extends Object
A collection of methods to read and write special values to/from CRAM files.

  • Field Details

    • CRAM_FILE_EXTENSION

      @Deprecated public static final String CRAM_FILE_EXTENSION
      Deprecated.
      since June 2019 Use FileExtensions.CRAM instead.
      See Also:

    • ZERO_B_EOF_MARKER

      public static final byte[] ZERO_B_EOF_MARKER
      The 'zero-B' EOF marker as per CRAM specs v2.1. This is basically a serialized empty CRAM container with sequence id set to some number to spell out 'EOF' in hex.

    • ZERO_F_EOF_MARKER

      public static final byte[] ZERO_F_EOF_MARKER
      The zero-F EOF marker as per CRAM specs v3.0. This is basically a serialized empty CRAM container with sequence id set to some number to spell out 'EOF' in hex.

    • EOF_ALIGNMENT_START

      public static final int EOF_ALIGNMENT_START
      See Also:

    • EOF_BLOCK_SIZE_V3

      public static final int EOF_BLOCK_SIZE_V3
      See Also:

    • EOF_BLOCK_SIZE_V2

      public static final int EOF_BLOCK_SIZE_V2
      See Also:

    • EOF_ALIGNMENT_SPAN

      public static final int EOF_ALIGNMENT_SPAN
      See Also:

  • Constructor Details

    • CramIO

      public CramIO()

  • Method Details

    • writeCramEOF

      public static long writeCramEOF(CRAMVersion cramVersion, OutputStream outputStream)
      Write an end-of-file marker to the OutputStream. The specific EOF marker is chosen based on the CRAM version. On read, this is interpreted as a special container sentinel indicating no more containers. The treatment of these EOF markers is asymmetric in that on read, the EOF marker is read in as a special container with sentinel values indicating it is an EOF container (as defined by the spec).
      Parameters:
      cramVersion - the CRAM version to assume
      outputStream - the stream to write to
      Returns:
      the number of bytes written out

    • writeCramHeader

      public static long writeCramHeader(CramHeader cramHeader, OutputStream outputStream)
      Writes CRAM header into the specified OutputStream.
      Parameters:
      cramHeader - the CramHeader object to write
      outputStream - the output stream to write to
      Returns:
      the number of bytes written out

    • readCramHeader

      public static CramHeader readCramHeader(InputStream inputStream)
      Read CRAM header from the given InputStream.
      Parameters:
      inputStream - input stream to read from
      Returns:
      complete CramHeader object

    • samHeaderToByteArray

      public static byte[] samHeaderToByteArray(SAMFileHeader samFileHeader)