Package htsjdk.beta.plugin.variants

Class VariantsDecoderOptions

java.lang.Object
htsjdk.beta.plugin.variants.VariantsDecoderOptions
All Implemented Interfaces:
HtsDecoderOptions
public class VariantsDecoderOptions extends Object implements HtsDecoderOptions

  • Constructor Details

    • VariantsDecoderOptions

      public VariantsDecoderOptions()

  • Method Details

    • getVariantsChannelTransformer

      @InternalAPI public Optional<Function<SeekableByteChannel,SeekableByteChannel>> getVariantsChannelTransformer()
      Get the channel transformer for the variants resource. The channel transformer can be used to implement prefetching for the variants input.
      Returns:
      the channel transformer for the reads resource if present, otherwise Optional.empty()

    • setVariantsChannelTransformer

      @InternalAPI public VariantsDecoderOptions setVariantsChannelTransformer(Function<SeekableByteChannel,SeekableByteChannel> variantsChannelTransformer)
      Set the channel transformer for the variants resource. The channel transformer can be used to implement prefetching for the variants input.
      Parameters:
      variantsChannelTransformer - the channel transformer to be used. may be null
      Returns:
      updated VariantsDecoderOptions

    • getIndexChannelTransformer

      @InternalAPI public Optional<Function<SeekableByteChannel,SeekableByteChannel>> getIndexChannelTransformer()
      Get the channel transformer for the index resource. The channel transformer can be used to implement prefetching for the index input.
      Returns:
      the channel transformer for the index resource if present, otherwise Optional.empty()

    • setIndexChannelTransformer

      @InternalAPI public VariantsDecoderOptions setIndexChannelTransformer(Function<SeekableByteChannel,SeekableByteChannel> indexChannelTransformer)
      Set the channel transformer for the index resource. The channel transformer can be used to implement prefetching for the index input.
      Parameters:
      indexChannelTransformer - the channel transformer to be used. may be null.
      Returns:
      updated VariantsDecoderOptions