htsjdk.samtools.cram.encoding.core

Class CoreCodec<T>

java.lang.Object

htsjdk.samtools.cram.encoding.core.CoreCodec<T>

Type Parameters:

T - data series type to be read or written

All Implemented Interfaces:

CRAMCodec<T>

Direct Known Subclasses:

BetaIntegerCodec

public abstract class CoreCodec<T>
extends java.lang.Object
implements CRAMCodec<T>

Superclass of Codecs which operate on Core Block bit streams Contrast with ExternalCodec for External Block byte streams

Field Summary

Fields

Modifier and Type	Field and Description
protected BitInputStream	coreBlockInputStream
protected BitOutputStream	coreBlockOutputStream

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CoreCodec(BitInputStream coreBlockInputStream, BitOutputStream coreBlockOutputStream) Create a new CoreCodec with associated input and output bit streams

Method Summary

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.cram.encoding.CRAMCodec

read, read, write

Field Detail

coreBlockInputStream

protected final BitInputStream coreBlockInputStream

coreBlockOutputStream

protected final BitOutputStream coreBlockOutputStream

Constructor Detail

CoreCodec

protected CoreCodec(BitInputStream coreBlockInputStream,
                    BitOutputStream coreBlockOutputStream)

Create a new CoreCodec with associated input and output bit streams

Parameters:

coreBlockInputStream - bit stream for reading input

coreBlockOutputStream - bit stream for writing output