Package 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 Details

    • VariantsResolver

      public VariantsResolver()
      Create a VariantsResolver.

  • Method Details

    • 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, 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.