htsjdk.beta.plugin.registry

Class HaploidReferenceResolver

java.lang.Object

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

htsjdk.beta.plugin.registry.HaploidReferenceResolver

public class HaploidReferenceResolver
extends HtsCodecResolver<HaploidReferenceCodec>

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

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

Provides typesafe conversion of argument and return types to types that conform to those used by HaploidReferenceCodecs, such as HaploidReferenceDecoder and HaploidReferenceEncoder.

Constructor Summary

Constructors

Constructor and Description
HaploidReferenceResolver() Create a new HaploidReferenceResolver.

Method Summary

Modifier and Type	Method and Description
HaploidReferenceDecoder	getHaploidReferenceDecoder(Bundle inputBundle) Get a HaploidReferenceDecoder for the given input Bundle.
HaploidReferenceDecoder	getHaploidReferenceDecoder(Bundle inputBundle, HaploidReferenceDecoderOptions HaploidReferenceDecoderOptions) Get a HaploidReferenceDecoder suitable for decoding inputBundle using options in HaploidReferenceDecoderOptions.
HaploidReferenceDecoder	getHaploidReferenceDecoder(IOPath inputPath) Get a HaploidReferenceDecoder for the given inputPath.
HaploidReferenceDecoder	getHaploidReferenceDecoder(IOPath inputPath, HaploidReferenceDecoderOptions HaploidReferenceDecoderOptions) Get a HaploidReferenceDecoder suitable for decoding inputPath using options in HaploidReferenceDecoderOptions.

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

HaploidReferenceResolver

public HaploidReferenceResolver()

Create a new HaploidReferenceResolver.

Method Detail

getHaploidReferenceDecoder

public HaploidReferenceDecoder getHaploidReferenceDecoder(IOPath inputPath)

Get a HaploidReferenceDecoder for the given inputPath.

Parameters:

inputPath - the path to the resource to be decoded

Returns:

a HaploidReferenceDecoder for the given 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.

getHaploidReferenceDecoder

public HaploidReferenceDecoder getHaploidReferenceDecoder(IOPath inputPath,
                                                          HaploidReferenceDecoderOptions HaploidReferenceDecoderOptions)

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

Parameters:

inputPath - the IOPath to be decoded

HaploidReferenceDecoderOptions - options to use

Returns:

a HaploidReferenceDecoder 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.

getHaploidReferenceDecoder

public HaploidReferenceDecoder getHaploidReferenceDecoder(Bundle inputBundle)

Get a HaploidReferenceDecoder for the given input Bundle.

Parameters:

inputBundle - the path to the bundle containing the resource to be decoded

Returns:

a HaploidReferenceDecoder for the given 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.

getHaploidReferenceDecoder

public HaploidReferenceDecoder getHaploidReferenceDecoder(Bundle inputBundle,
                                                          HaploidReferenceDecoderOptions HaploidReferenceDecoderOptions)

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

Parameters:

inputBundle - the bundle to be decoded

HaploidReferenceDecoderOptions - HaploidReferenceDecoderOptions options to be used by the decoder

Returns:

a HaploidReferenceDecoder 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.