htsjdk.beta.plugin.registry

Class VariantsResolver

java.lang.Object

htsjdk.beta.plugin.registry.HtsCodecResolver<VariantsCodec>

htsjdk.beta.plugin.registry.VariantsResolver

public class VariantsResolver
extends HtsCodecResolver<VariantsCodec>

Class with methods for resolving inputs and outputs to variants encoders and decoders.

Provides a convenient typesafe layer over the HtsCodecResolver used by an HtsCodecRegistry to manage VariantsCodecs (see HtsCodecRegistry.getHaploidReferenceResolver()).

Provides typesafe conversion of argument and return types to types that conform to those used with VariantsCodecs, such as VariantsDecoder, VariantsEncoder, VariantsDecoderOptions.

Constructor Summary

Constructors

Constructor and Description
VariantsResolver() Create a VariantsResolver.

Method Summary

Modifier and Type	Method and Description
VariantsDecoder	getVariantsDecoder(Bundle inputBundle) Get a VariantsDecoder suitable for decoding inputBundle.
VariantsDecoder	getVariantsDecoder(Bundle inputBundle, VariantsDecoderOptions variantsDecoderOptions) Get a VariantsDecoder suitable for decoding inputBundle using variantsDecoderOptions.
VariantsDecoder	getVariantsDecoder(IOPath inputPath) Get a VariantsDecoder suitable for decoding inputPath.
VariantsDecoder	getVariantsDecoder(IOPath inputPath, VariantsDecoderOptions variantsDecoderOptions) Get a VariantsDecoder suitable for decoding inputPath using variantsDecoderOptions.
VariantsEncoder	getVariantsEncoder(Bundle outputBundle, VariantsEncoderOptions variantsEncoderOptions) Get a VariantsEncoder suitable for encoding to outputBundle using variantsEncoderOptions.
VariantsEncoder	getVariantsEncoder(Bundle outputBundle, VariantsEncoderOptions variantsEncoderOptions, java.lang.String variantsFormat, HtsVersion formatVersion) Get a VariantsEncoder suitable for encoding to outputBundle using variantsEncoderOptions, specifying a version and output format.
VariantsEncoder	getVariantsEncoder(IOPath outputPath) Get a VariantsEncoder suitable for encoding to outputPath.
VariantsEncoder	getVariantsEncoder(IOPath outputPath, VariantsEncoderOptions variantsEncoderOptions) Get a VariantsEncoder suitable for encoding to outputPath using variantsEncoderOptions.

Methods inherited from class htsjdk.beta.plugin.registry.HtsCodecResolver

getCodecs, registerCodec, resolveForDecoding, resolveForEncoding, resolveForEncoding, resolveForFormat, resolveFormatAndVersion

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantsResolver

public VariantsResolver()

Create a VariantsResolver.

Method Detail

getVariantsDecoder

public VariantsDecoder getVariantsDecoder(IOPath inputPath)

Get a VariantsDecoder suitable for decoding inputPath.

Parameters:

inputPath - the input path to decode

Returns:

a VariantsDecoder suitable for decoding inputPath

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsDecoder

public VariantsDecoder getVariantsDecoder(IOPath inputPath,
                                          VariantsDecoderOptions variantsDecoderOptions)

Get a VariantsDecoder suitable for decoding inputPath using variantsDecoderOptions.

Parameters:

inputPath - the input path to decode

variantsDecoderOptions - decoder options to use

Returns:

a VariantsDecoder suitable for decoding inputPath

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsDecoder

public VariantsDecoder getVariantsDecoder(Bundle inputBundle)

Get a VariantsDecoder suitable for decoding inputBundle.

Parameters:

inputBundle - the input bundle containing resources to decode

Returns:

a VariantsDecoder suitable for decoding inputBundle

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsDecoder

public VariantsDecoder getVariantsDecoder(Bundle inputBundle,
                                          VariantsDecoderOptions variantsDecoderOptions)

Get a VariantsDecoder suitable for decoding inputBundle using variantsDecoderOptions.

Parameters:

inputBundle - the input bundle to decode

variantsDecoderOptions - decoder options to use

Returns:

a VariantsDecoder suitable for decoding inputBundle

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsEncoder

public VariantsEncoder getVariantsEncoder(IOPath outputPath)

Get a VariantsEncoder suitable for encoding to outputPath.

Parameters:

outputPath - path to encode to

Returns:

a VariantsEncoder suitable for encoding to outputPath

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsEncoder

public VariantsEncoder getVariantsEncoder(IOPath outputPath,
                                          VariantsEncoderOptions variantsEncoderOptions)

Get a VariantsEncoder suitable for encoding to outputPath using variantsEncoderOptions.

Parameters:

outputPath - path to encode to

variantsEncoderOptions - encoder options to use

Returns:

a VariantsEncoder suitable for encoding to outputPath

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsEncoder

public VariantsEncoder getVariantsEncoder(Bundle outputBundle,
                                          VariantsEncoderOptions variantsEncoderOptions)

Get a VariantsEncoder suitable for encoding to outputBundle using variantsEncoderOptions.

Parameters:

outputBundle - output bundle containg resources to encode to

variantsEncoderOptions - options to use

Returns:

a VariantsEncoder suitable for encoding to outputBundle

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.

getVariantsEncoder

public VariantsEncoder getVariantsEncoder(Bundle outputBundle,
                                          VariantsEncoderOptions variantsEncoderOptions,
                                          java.lang.String variantsFormat,
                                          HtsVersion formatVersion)

Get a VariantsEncoder suitable for encoding to outputBundle using variantsEncoderOptions, specifying a version and output format.

Parameters:

outputBundle - output bundle containing resources to encode to

variantsEncoderOptions - options to use

variantsFormat - the output format to use

formatVersion - the format version to use

Returns:

a VariantsEncoder suitable for encoding to outputBundle

Throws:

HtsjdkException - if no registered codecs can handle the resource

HtsjdkPluginException - if more than one codec claims to handle the resource. this usually indicates that the registry contains an incorrectly written codec.