htsjdk.beta.codecs.variants.vcf.vcfv4_2

Class VCFCodecV4_2

java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFCodec

htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2

All Implemented Interfaces:

HtsCodec<VariantsDecoderOptions,VariantsEncoderOptions>, Upgradeable, VariantsCodec

public class VCFCodecV4_2
extends VCFCodec

VCF V4.2 codec.

Field Summary

Fields

Modifier and Type	Field and Description
static HtsVersion	VCF_V42_VERSION

Constructor Summary

Constructors

Constructor and Description
VCFCodecV4_2()

Method Summary

Modifier and Type	Method and Description
VCFDecoder	getDecoder(Bundle inputBundle, VariantsDecoderOptions decoderOptions) Get an HtsDecoder to decode the provided inputs.
VCFEncoder	getEncoder(Bundle outputBundle, VariantsEncoderOptions encoderOptions) Get an HtsEncoder to encode to the provided outputs.
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.
boolean	runVersionUpgrade(HtsVersion sourceCodecVersion, HtsVersion targetCodecVersion)

Methods inherited from class htsjdk.beta.codecs.variants.vcf.VCFCodec

canDecodeSignature, canDecodeURI, getFileFormat, getSignatureLength, getSignatureProbeLength

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.variants.VariantsCodec

getContentType

Methods inherited from interface htsjdk.beta.plugin.HtsCodec

getDisplayName, ownsURI

Field Detail

VCF_V42_VERSION

public static final HtsVersion VCF_V42_VERSION

Constructor Detail

VCFCodecV4_2

public VCFCodecV4_2()

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

getDecoder

public VCFDecoder getDecoder(Bundle inputBundle,
                             VariantsDecoderOptions decoderOptions)

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.

decoderOptions - options for the decoder to use

Returns:

an HtsDecoder that can decode the provided inputs

getEncoder

public VCFEncoder getEncoder(Bundle outputBundle,
                             VariantsEncoderOptions encoderOptions)

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

encoderOptions - encoder options to use

Returns:

an HtsEncoder suitable for writing to the provided outputs

runVersionUpgrade

public boolean runVersionUpgrade(HtsVersion sourceCodecVersion,
                                 HtsVersion targetCodecVersion)

getSignatureString

protected java.lang.String getSignatureString()

Description copied from class: VCFCodec

Get the signature string for this codec.

Specified by:

getSignatureString in class VCFCodec

Returns:

the signature string for this codec