htsjdk.samtools.cram.io

Class ITF8

java.lang.Object

htsjdk.samtools.cram.io.ITF8

public class ITF8
extends java.lang.Object

Methods to read and write int values as per ITF8 specification in CRAM. ITF8 encodes ints as 1 to 5 bytes depending on the highest set bit. (using 1-based counting) If highest bit < 8: write out [bits 1-8] Highest bit = 8-14: write a byte 1,0,[bits 9-14] write out [bits 1-8] Highest bit = 15-21: write a byte 1,1,0,[bits 17-21] write out [bits 9-16] write out [bits 1-8] Highest bit = 22-28: write a byte 1,1,1,0,[bits 25-28] write out [bits 17-24] write out [bits 9-16] write out [bits 1-8] Highest bit > 28: write a byte 1,1,1,1,[bits 29-32] write out [bits 21-28] **** note the change in pattern here write out [bits 13-20] write out [bits 5-12] write out [bits 1-8]

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_BYTES

Constructor Summary

Constructors

Constructor and Description
ITF8()

Method Summary

Modifier and Type	Method and Description
static int	readUnsignedITF8(byte[] data) Reads an unsigned (32 bit) integer from an array of bytes.
static int	readUnsignedITF8(java.nio.ByteBuffer buffer) Reads an unsigned (32 bit) integer from a ByteBuffer.
static int	readUnsignedITF8(java.io.InputStream inputStream) Reads an unsigned (32 bit) integer from an InputStream.
static byte[]	writeUnsignedITF8(int value) Writes an unsigned (32 bit) integer to a byte new array encoded as ITF8.
static int	writeUnsignedITF8(int value, java.nio.ByteBuffer buffer) Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8.
static int	writeUnsignedITF8(int value, java.io.OutputStream outputStream) Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_BYTES

public static final int MAX_BYTES

See Also:

Constant Field Values

Constructor Detail

ITF8

public ITF8()

Method Detail

readUnsignedITF8

public static int readUnsignedITF8(java.io.InputStream inputStream)

Reads an unsigned (32 bit) integer from an InputStream. The sign bit should be interpreted as a value bit.

Parameters:

inputStream - the stream to read from

Returns:

the value read

readUnsignedITF8

public static int readUnsignedITF8(java.nio.ByteBuffer buffer)

Reads an unsigned (32 bit) integer from a ByteBuffer. The sign bit should be interpreted as a value bit.

Parameters:

buffer - the bytes to read from

Returns:

unsigned integer value from the buffer

readUnsignedITF8

public static int readUnsignedITF8(byte[] data)

Reads an unsigned (32 bit) integer from an array of bytes. The sign bit should be interpreted as a value bit.

Parameters:

data - the bytes to read from

Returns:

the value read

writeUnsignedITF8

public static int writeUnsignedITF8(int value,
                                    java.io.OutputStream outputStream)

Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8. The sign bit is interpreted as a value bit.

Parameters:

value - the value to be written out

outputStream - the stream to write to

Returns:

number of bits written

writeUnsignedITF8

public static int writeUnsignedITF8(int value,
                                    java.nio.ByteBuffer buffer)

Writes an unsigned (32 bit) integer to an OutputStream encoded as ITF8. The sign bit is interpreted as a value bit.

Parameters:

value - the value to be written out

buffer - the ByteBuffer to write to

writeUnsignedITF8

public static byte[] writeUnsignedITF8(int value)

Writes an unsigned (32 bit) integer to a byte new array encoded as ITF8. The sign bit is interpreted as a value bit.

Parameters:

value - the value to be written out

Returns:

the bytes holding ITF8 representation of the value