Package htsjdk.beta.plugin.reads

Class ReadsDecoderOptions

java.lang.Object
htsjdk.beta.plugin.reads.ReadsDecoderOptions
All Implemented Interfaces:
HtsDecoderOptions
public class ReadsDecoderOptions extends Object implements HtsDecoderOptions
Reads decoder options (shared/common).

  • Constructor Details

    • ReadsDecoderOptions

      public ReadsDecoderOptions()

  • Method Details

    • getValidationStringency

      public ValidationStringency getValidationStringency()
      Get the ValidationStringency used for these options. Defaults to ValidationStringency.STRICT.
      Returns:
      the ValidationStringency used for these options

    • setValidationStringency

      public ReadsDecoderOptions setValidationStringency(ValidationStringency validationStringency)
      Set the ValidationStringency used for these options. Defaults value is ValidationStringency.STRICT.
      Parameters:
      validationStringency - the ValidationStringency used for these options
      Returns:
      updated ReadsDecoderOptions

    • isDecodeEagerly

      public boolean isDecodeEagerly()
      Get eagerly decoding state used for these options.
      Returns:
      true if eager decoding is enabled, otherwise false

    • setDecodeEagerly

      public ReadsDecoderOptions setDecodeEagerly(boolean eagerlyDecode)
      Set the eagerly decoding state used for these options.
      Parameters:
      eagerlyDecode - true if eagerly decode is set, otherwise false
      Returns:
      updated ReadsDecoderOptions

    • isFileBasedIndexCached

      public boolean isFileBasedIndexCached()
      Get the file based index cache setting used for these options.
      Returns:
      true if caching is enabled for index files, otherwise false

    • setFileBasedIndexCached

      public ReadsDecoderOptions setFileBasedIndexCached(boolean fileBasedIndexCached)
      Set id file based index caching is enabled for these options.
      Parameters:
      fileBasedIndexCached - true to enable caching, otherwise false
      Returns:
      updated ReadsDecoderOptions

    • isMemoryMapIndexes

      public boolean isMemoryMapIndexes()
      Get whether mapping indexes is enabled. Defaults to true.
      Returns:
      true if indexes are memory mapped, otherwise false

    • setMemoryMapIndexes

      public ReadsDecoderOptions setMemoryMapIndexes(boolean memoryMapIndexes)
      Set whether memory mapping indexes is enabled. Defaults to true.
      Parameters:
      memoryMapIndexes - true if indexes are memory mapped, otherwise false
      Returns:
      updated ReadsDecoderOptions

    • getBAMDecoderOptions

      public BAMDecoderOptions getBAMDecoderOptions()
      Get the BAMDecoderOptions for these options.
      Returns:
      the BAMDecoderOptions for these options

    • setBAMDecoderOptions

      public ReadsDecoderOptions setBAMDecoderOptions(BAMDecoderOptions bamDecoderOptions)
      Set the BAMDecoderOptions used for these options.
      Parameters:
      bamDecoderOptions - the BAMDecoderOptions for these ReadsDecoderOptions
      Returns:
      updated ReadsDecoderOptions

    • getCRAMDecoderOptions

      public CRAMDecoderOptions getCRAMDecoderOptions()
      Get the CRAMDecoderOptions for these options.
      Returns:
      the CRAMDecoderOptions for these options

    • setCRAMDecoderOptions

      public ReadsDecoderOptions setCRAMDecoderOptions(CRAMDecoderOptions cramDecoderOptions)
      Set the CRAMDecoderOptions for these ReadsDecoderOptions.
      Parameters:
      cramDecoderOptions - the CRAMDecoderOptions for these ReadsDecoderOptions
      Returns:
      updated ReadsDecoderOptions

    • getReadsChannelTransformer

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

    • setReadsChannelTransformer

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

    • 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 ReadsDecoderOptions 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 ReadsDecoderOptions