htsjdk.beta.codecs.reads.cram.cramV3_0

Class CRAMCodecV3_0

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMCodec

htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0

All Implemented Interfaces:

HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>, ReadsCodec, Upgradeable

public class CRAMCodecV3_0
extends CRAMCodec

CRAM v3.0 codec

Field Summary

Fields

Modifier and Type	Field and Description
static HtsVersion	VERSION_3_0

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

extensionMap

Constructor Summary

Constructors

Constructor and Description
CRAMCodecV3_0()

Method Summary

Modifier and Type	Method and Description
boolean	canDecodeSignature(SignatureStream signatureStream, java.lang.String sourceName) Determine if the codec can decode an input stream by inspecting a signature embedded within the stream.
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

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_3_0

public static final HtsVersion VERSION_3_0

Constructor Detail

CRAMCodecV3_0

public CRAMCodecV3_0()

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.

canDecodeSignature

public boolean canDecodeSignature(SignatureStream signatureStream,
                                  java.lang.String sourceName)

Description copied from interface: HtsCodec

Determine if the codec can decode an input stream by inspecting a signature embedded within the stream.

The probingInputStream stream will contain only a fragment of the actual input stream, taken from the start of the stream, the size of which will be the lesser of:

1. the number of bytes returned by HtsCodec.getSignatureProbeLength()
2. the entire input stream, for streams that are smaller than HtsCodec.getSignatureProbeLength()

Codecs that handle custom URIs that reference remote resources (those that return true for HtsCodec.ownsURI(htsjdk.io.IOPath)) should generally not inspect the stream, and should return false from this method, since the method will never be called with any resource for which HtsCodec.ownsURI(htsjdk.io.IOPath) returned true. Since this method is used during codec resolution, implementations should avoid calling methods that may throw exceptions.

Specified by:

canDecodeSignature in interface HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>

Overrides:

canDecodeSignature in class CRAMCodec

Parameters:

signatureStream - the stream to be inspect for the resource's embedded signature and version

sourceName - a display name describing the source of the input stream, for use in error messages

Returns:

true if this codec recognizes the stream by it's signature, and can provide a decoder to decode the stream, otherwise false

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