java.lang.Object
- htsjdk.samtools.cram.encoding.CRAMEncoding<T>

Type Parameters:

T - data series type

Direct Known Subclasses:

BetaIntegerEncoding, ByteArrayLenEncoding, ByteArrayStopEncoding, CanonicalHuffmanByteEncoding, CanonicalHuffmanIntegerEncoding, ExternalByteArrayEncoding, ExternalByteEncoding, ExternalIntegerEncoding, ExternalLongEncoding, GammaIntegerEncoding, GolombIntegerEncoding, GolombLongEncoding, GolombRiceIntegerEncoding, SubexponentialIntegerEncoding
```
public abstract class CRAMEncoding<T>
extends Object
```
An interface to describe how a data series is encoded. It also has methods to serialize/deserialize its parameters to/from a byte array and a method to construct a CRAMCodec instance.

Constructor Summary

Constructors
Modifier Constructor Description

protected CRAMEncoding(EncodingID id)
Create a new encoding.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract CRAMCodec<T>`	`buildCodec(BitInputStream coreBlockInputStream, BitOutputStream coreBlockOutputStream, Map<Integer,ByteArrayInputStream> externalBlockInputMap, Map<Integer,ByteArrayOutputStream> externalBlockOutputMap)`	Instantiate the codec represented by this encoding by supplying it with the appropriate streams
`CRAMCodec<T>`	`buildReadCodec(BitInputStream coreBlockInputStream, Map<Integer,ByteArrayInputStream> externalBlockInputMap)`	Convenience initializer method for read codecs
`CRAMCodec<T>`	`buildWriteCodec(BitOutputStream coreBlockOutputStream, Map<Integer,ByteArrayOutputStream> externalBlockOutputMap)`	Convenience initializer method for write codecs
`EncodingID`	`id()`
`abstract byte[]`	`toByteArray()`	Subclasses but have a defined serialization of their parameters
`EncodingParams`	`toParam()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CRAMEncoding
```
protected CRAMEncoding(EncodingID id)
```
    Create a new encoding. Concrete implementation constructors will specify their parameters
    
    Parameters:
    
    id - the EncodingID associated with the concrete implementation
- Method Detail
  - id
```
public EncodingID id()
```
  - toParam
```
public EncodingParams toParam()
```
  - toByteArray
```
public abstract byte[] toByteArray()
```
    Subclasses but have a defined serialization of their parameters
    
    Returns:
    
    a byte array representing a specific encoding's parameter values
  - buildCodec
```
public abstract CRAMCodec<T> buildCodec(BitInputStream coreBlockInputStream,
                                        BitOutputStream coreBlockOutputStream,
                                        Map<Integer,ByteArrayInputStream> externalBlockInputMap,
                                        Map<Integer,ByteArrayOutputStream> externalBlockOutputMap)
```
    Instantiate the codec represented by this encoding by supplying it with the appropriate streams
    
    Parameters:
    
    coreBlockInputStream - the core block bit stream a CoreCodec will read from
    
    coreBlockOutputStream - the core block bit stream a CoreCodec will write to
    
    externalBlockInputMap - the external block byte stream a ExternalCodec will read from
    
    externalBlockOutputMap - the external block byte stream a ExternalCodec will write to
    
    Returns:
    
    a newly instantiated codec
  - buildReadCodec
```
public CRAMCodec<T> buildReadCodec(BitInputStream coreBlockInputStream,
                                   Map<Integer,ByteArrayInputStream> externalBlockInputMap)
```
    Convenience initializer method for read codecs
    
    Parameters:
    
    coreBlockInputStream - the core block bit stream a CoreCodec will read from
    
    externalBlockInputMap - the external block byte stream a ExternalCodec will read from
    
    Returns:
  - buildWriteCodec
```
public CRAMCodec<T> buildWriteCodec(BitOutputStream coreBlockOutputStream,
                                    Map<Integer,ByteArrayOutputStream> externalBlockOutputMap)
```
    Convenience initializer method for write codecs
    
    Parameters:
    
    coreBlockOutputStream - the core block bit stream a CoreCodec will write to
    
    externalBlockOutputMap - the external block byte stream a ExternalCodec will write to
    
    Returns:

Class CRAMEncoding<T>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CRAMEncoding

Method Detail

id

toParam

toByteArray

buildCodec

buildReadCodec

buildWriteCodec