htsjdk.samtools.util

Class BlockCompressedFilePointerUtil

java.lang.Object

htsjdk.samtools.util.BlockCompressedFilePointerUtil

public class BlockCompressedFilePointerUtil
extends java.lang.Object

Static for manipulating virtual file pointers in BGZF files.

Field Summary

Fields

Modifier and Type	Field and Description
static long	MAX_BLOCK_ADDRESS
static int	MAX_OFFSET

Constructor Summary

Constructors

Constructor and Description
BlockCompressedFilePointerUtil()

Method Summary

Modifier and Type	Method and Description
static boolean	areInSameOrAdjacentBlocks(long vfp1, long vfp2)
static java.lang.String	asAddressOffsetString(long vfp) Return a String with the file pointer in "address:offset" form.
static java.lang.String	asString(long vfp)
static int	compare(long vfp1, long vfp2)
static long	getBlockAddress(long virtualFilePointer)
static int	getBlockOffset(long virtualFilePointer)
static long	makeFilePointer(long blockAddress)
static long	makeFilePointer(long blockAddress, int blockOffset)
static long	shift(long virtualFilePointer, long offset) Move a virtual file pointer by a given (non-virtual) offset.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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 java.lang.String asString(long vfp)

asAddressOffsetString

public static java.lang.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