Field Detail

• MAX_BLOCK_ADDRESS

  public static final long MAX_BLOCK_ADDRESS

  See Also:

  Constant Field Values

• MAX_OFFSET

  public static final int MAX_OFFSET

  See Also:

  Constant Field Values

Constructor Detail

• BlockCompressedFilePointerUtil

  public BlockCompressedFilePointerUtil()

Method Detail

• compare

  public static int compare​(long vfp1,
                            long vfp2)

  Parameters:

  vfp1 -

  vfp2 -

  Returns:

  negative if vfp1 is earlier in file than vfp2, positive if it is later, 0 if equal.

• areInSameOrAdjacentBlocks

  public static boolean areInSameOrAdjacentBlocks​(long vfp1,
                                                  long vfp2)

  Returns:

  true if vfp2 points to somewhere in the same BGZF block, or the one immediately following vfp1's BGZF block.

• makeFilePointer

  public static long makeFilePointer​(long blockAddress)

  Parameters:

  blockAddress - File offset of start of BGZF block.

  Returns:

  Virtual file pointer that points to the start of a BGZF block.

• makeFilePointer

  public static long makeFilePointer​(long blockAddress,
                                     int blockOffset)

  Parameters:

  blockAddress - File offset of start of BGZF block.

  blockOffset - Offset into uncompressed block.

  Returns:

  Virtual file pointer that embodies the input parameters.

• getBlockAddress

  public static long getBlockAddress​(long virtualFilePointer)

  Parameters:

  virtualFilePointer -

  Returns:

  File offset of start of BGZF block for this virtual file pointer.

• getBlockOffset

  public static int getBlockOffset​(long virtualFilePointer)

  Parameters:

  virtualFilePointer -

  Returns:

  Offset into uncompressed block for this virtual file pointer.

• shift

  public static long shift​(long virtualFilePointer,
                           long offset)

  Move a virtual file pointer by a given (non-virtual) offset.

  Parameters:

  virtualFilePointer - the original virtual file pointer

  offset - the offset in bytes

  Returns:

  a new virtual file pointer shifted by the given offset

• asString

  public static String asString​(long vfp)

• asAddressOffsetString

  public static String asAddressOffsetString​(long vfp)

  Return a String with the file pointer in "address:offset" form.

  Parameters:

  vfp - virtual file pointer to format

  Returns:

  vfp formatted as string in address:offset form