htsjdk.samtools.cram.encoding.external

Class ByteArrayStopCodec

java.lang.Object

htsjdk.samtools.cram.encoding.external.ExternalCodec<byte[]>

htsjdk.samtools.cram.encoding.external.ByteArrayStopCodec

All Implemented Interfaces:

CRAMCodec<byte[]>

public class ByteArrayStopCodec
extends ExternalCodec<byte[]>

Encode byte arrays by specifying a stop byte to separate the arrays. This cannot be a byte that appears in the data.

Field Summary

Fields inherited from class htsjdk.samtools.cram.encoding.external.ExternalCodec

inputStream, outputStream

Constructor Summary

Constructors

Constructor and Description
ByteArrayStopCodec(java.io.ByteArrayInputStream inputStream, java.io.ByteArrayOutputStream outputStream, byte stopByte) Construct a Byte Array Stop Codec

Method Summary

Modifier and Type	Method and Description
byte[]	read() Read a single object from the stream
byte[]	read(int length) Read a array of specified length from the stream
void	write(byte[] value) Write an object to the stream

Methods inherited from class java.lang.Object

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

Constructor Detail

ByteArrayStopCodec

public ByteArrayStopCodec(java.io.ByteArrayInputStream inputStream,
                          java.io.ByteArrayOutputStream outputStream,
                          byte stopByte)

Construct a Byte Array Stop Codec

Parameters:

inputStream - the input bytestream to read from

outputStream - the output bytestream to write to

stopByte - the byte used to mark array boundaries

Method Detail

read

public byte[] read()

Description copied from interface: CRAMCodec

Read a single object from the stream

Returns:

an object from the stream

read

public byte[] read(int length)

Description copied from interface: CRAMCodec

Read a array of specified length from the stream

Parameters:

length - the number of elements to read

Returns:

an object from the stream

write

public void write(byte[] value)

Description copied from interface: CRAMCodec

Write an object to the stream

Parameters:

value - the object to write