Package 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 Details

    • ReadsResolver

      public ReadsResolver()
      Create a ReadsResolver.

  • Method Details

    • 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, 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.

    • filterByVersion

      protected List<ReadsCodec> filterByVersion(List<ReadsCodec> candidateCodecs, HtsVersion htsVersion)
      Temporarily override to remove the CRAM 3.1 codec from the list of candidate codecs when the request is for the newest version, since it has no write implementation yet.
      Overrides:
      filterByVersion in class HtsCodecResolver<ReadsCodec>