htsjdk.beta.plugin.registry

Class ReadsResolver

java.lang.Object

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

htsjdk.beta.plugin.registry.ReadsResolver

public class ReadsResolver
extends HtsCodecResolver<ReadsCodec>

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

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

Provides typesafe conversion of argument and return types to types that conform to those used with ReadsCodecs, such as ReadsDecoder, ReadsEncoder, ReadsDecoderOptions.

Constructor Summary

Constructors

Constructor and Description
ReadsResolver() Create a ReadsResolver.

Method Summary

Modifier and Type	Method and Description
ReadsDecoder	getReadsDecoder(Bundle inputBundle) Get a ReadsDecoder suitable for decoding inputBundle.
ReadsDecoder	getReadsDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Get a ReadsDecoder suitable for decoding inputBundle using options in readsDecoderOptions.
ReadsDecoder	getReadsDecoder(IOPath inputPath) Get a ReadsDecoder suitable for decoding inputPath.
ReadsDecoder	getReadsDecoder(IOPath inputPath, ReadsDecoderOptions readsDecoderOptions) Grt a ReadsDecoder suitable for decoding inputPath using options in readsDecoderOptions.
ReadsEncoder	getReadsEncoder(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) Get a ReadsEncoder suitable for encoding to outputBundle, using the options in readsEncoderOptions.
ReadsEncoder	getReadsEncoder(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions, java.lang.String readsFormat, HtsVersion formatVersion) Get a ReadsEncoder suitable for encoding to outputBundle, using the options in readsEncoderOptions, and the file format and version specified in readsFormat and formatVersion.
ReadsEncoder	getReadsEncoder(IOPath outputPath) Get a ReadsEncoder suitable for encoding to outputPath.
ReadsEncoder	getReadsEncoder(IOPath outputPath, ReadsEncoderOptions readsEncoderOptions) Get a ReadsEncoder suitable for encoding to outputPath, using the options in readsEncoderOptions.

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

ReadsResolver

public ReadsResolver()

Create a ReadsResolver.

Method Detail

getReadsDecoder

public ReadsDecoder getReadsDecoder(IOPath inputPath)

Get a ReadsDecoder suitable for decoding inputPath. The inputPath is inspected to determine the appropriate file format/version. The index is automatically resolved. To bypass index resolution, use getReadsDecoder(htsjdk.io.IOPath).

Parameters:

inputPath - the IOPath to be decoded

Returns:

a ReadsDecoder 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.

getReadsDecoder

public ReadsDecoder getReadsDecoder(IOPath inputPath,
                                    ReadsDecoderOptions readsDecoderOptions)

Grt a ReadsDecoder suitable for decoding inputPath using options in readsDecoderOptions. The inputPath is inspected to determine the appropriate file format/version. The index is automatically resolved. To bypass index resolution, use getReadsDecoder(htsjdk.io.IOPath).

Parameters:

inputPath - the IOPath to be decoded

readsDecoderOptions - options to use

Returns:

a ReadsDecoder 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.

getReadsDecoder

public ReadsDecoder getReadsDecoder(Bundle inputBundle)

Get a ReadsDecoder suitable for decoding inputBundle. The inputBundle is inspected to determine the appropriate file format/version.

Parameters:

inputBundle - the bundle to be decoded

Returns:

a ReadsDecoder 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.

getReadsDecoder

public ReadsDecoder getReadsDecoder(Bundle inputBundle,
                                    ReadsDecoderOptions readsDecoderOptions)

Get a ReadsDecoder suitable for decoding inputBundle using options in readsDecoderOptions. The inputBundle is inspected to determine the appropriate file format/version.

Parameters:

inputBundle - the bundle to be decoded

readsDecoderOptions - ReadsDecoderOptions options to be used by the decoder

Returns:

a ReadsDecoder 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.

getReadsEncoder

public ReadsEncoder getReadsEncoder(IOPath outputPath)

Get a ReadsEncoder suitable for encoding to outputPath. The path must include a file extension suitable for determining the appropriate file format to use; the newest version of the file format available will be used. To request a specific file format and/or version, use getReadsEncoder(Bundle, ReadsEncoderOptions, String, HtsVersion).

Parameters:

outputPath - the IOPath target for encoding

Returns:

a ReadsEncoder 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.

getReadsEncoder

public ReadsEncoder getReadsEncoder(IOPath outputPath,
                                    ReadsEncoderOptions readsEncoderOptions)

Get a ReadsEncoder suitable for encoding to outputPath, using the options in readsEncoderOptions. The path must include a file extension suitable for determining the appropriate file format to use; the newest version of the file format available will be used. To request a specific file format and/or version, use getReadsEncoder(Bundle, ReadsEncoderOptions, String, HtsVersion).

Parameters:

outputPath - target path to encode

readsEncoderOptions - ReadsEncoderOptions options to be used by the encoder

Returns:

ReadsEncoder 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.

getReadsEncoder

public ReadsEncoder getReadsEncoder(Bundle outputBundle,
                                    ReadsEncoderOptions readsEncoderOptions)

Get a ReadsEncoder suitable for encoding to outputBundle, using the options in readsEncoderOptions. The outputBundle must include a primary resource with a file extension suitable for determining the appropriate file format to use; or the resource must include a format. The newest version of the selected file format available will be used. To request a specific file format and/or version, use getReadsEncoder(Bundle, ReadsEncoderOptions, String, HtsVersion).

Parameters:

outputBundle - target output to encode to

readsEncoderOptions - ReadsEncoderOptions to be used by the encoder

Returns:

ReadsEncoder 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.

getReadsEncoder

public ReadsEncoder getReadsEncoder(Bundle outputBundle,
                                    ReadsEncoderOptions readsEncoderOptions,
                                    java.lang.String readsFormat,
                                    HtsVersion formatVersion)

Get a ReadsEncoder suitable for encoding to outputBundle, using the options in readsEncoderOptions, and the file format and version specified in readsFormat and formatVersion.

Parameters:

outputBundle - target output bundle

readsEncoderOptions - encode options to be used by the encoder

readsFormat - target file format

formatVersion - target file format version

Returns:

ReadsEncoder 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.