htsjdk.beta.codecs.reads.cram.cramV2_1

Class CRAMCodecV2_1

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMCodec

htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1

All Implemented Interfaces:

HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>, ReadsCodec, Upgradeable

public class CRAMCodecV2_1
extends CRAMCodec

CRAM v2.1 codec

Field Summary

Fields

Modifier and Type	Field and Description
static HtsVersion	VERSION_2_1

Fields inherited from class htsjdk.beta.codecs.reads.cram.CRAMCodec

extensionMap

Constructor Summary

Constructors

Constructor and Description
CRAMCodecV2_1()

Method Summary

Modifier and Type	Method and Description
CRAMDecoder	getDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Get an HtsDecoder to decode the provided inputs.
CRAMEncoder	getEncoder(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) Get an HtsEncoder to encode to the provided outputs.
int	getSignatureLength() Get the number of bytes in the format and version signature used by the file format supported by this codec.
protected java.lang.String	getSignatureString() Get the signature string for this codec.
HtsVersion	getVersion() Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.

Methods inherited from class htsjdk.beta.codecs.reads.cram.CRAMCodec

canDecodeSignature, canDecodeURI, getFileFormat, runVersionUpgrade

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.reads.ReadsCodec

getContentType

Methods inherited from interface htsjdk.beta.plugin.HtsCodec

getDisplayName, getSignatureProbeLength, ownsURI

Field Detail

VERSION_2_1

public static final HtsVersion VERSION_2_1

Constructor Detail

CRAMCodecV2_1

public CRAMCodecV2_1()

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsCodec

Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.

Returns:

the file format version (HtsVersion) supported by this codec

getSignatureLength

public int getSignatureLength()

Description copied from interface: HtsCodec

Get the number of bytes in the format and version signature used by the file format supported by this codec.

Returns:

if the file format supported by this codecs is not remote, and is accessible via a local file or stream, the size of the unique signature/version for this file format. otherwise 0.

Note: Codecs that are custom URI handlers (those that return true for HtsCodec.ownsURI(htsjdk.io.IOPath)), should always return 0 from this method. Since this method is used during codec resolution, implementations should avoid calling methods that may throw exceptions.

getDecoder

public CRAMDecoder getDecoder(Bundle inputBundle,
                              ReadsDecoderOptions readsDecoderOptions)

Description copied from interface: HtsCodec

Get an HtsDecoder to decode the provided inputs. The input bundle must contain resources of the type required by this codec. To find a codec appropriate for decoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call thi* method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) and HtsCodec.canDecodeSignature(SignatureStream, String) (IOPath)} return true for inputBundle.

Parameters:

inputBundle - input to be decoded. To get a decoder for use with index queries that use HtsQuery methods, the bundle must contain an index resource.

readsDecoderOptions - options for the decoder to use

Returns:

an HtsDecoder that can decode the provided inputs

getEncoder

public CRAMEncoder getEncoder(Bundle outputBundle,
                              ReadsEncoderOptions readsEncoderOptions)

Description copied from interface: HtsCodec

Get an HtsEncoder to encode to the provided outputs. The output bundle must contain resources of the type required by this codec. To find a codec appropriate for encoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call this method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) returned true for outputBundle.

Parameters:

outputBundle - target output for the encoder

readsEncoderOptions - encoder options to use

Returns:

an HtsEncoder suitable for writing to the provided outputs

getSignatureString

protected java.lang.String getSignatureString()

Description copied from class: CRAMCodec

Get the signature string for this codec.

Specified by:

getSignatureString in class CRAMCodec

Returns:

the signature string for this codec