Package htsjdk.beta.codecs.reads.bam

Class BAMDecoderOptions

java.lang.Object
htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
public class BAMDecoderOptions extends Object
Decoder options specific to BAM decoders.

  • Constructor Details

    • BAMDecoderOptions

      public BAMDecoderOptions()

  • Method Details

    • getInflaterFactory

      public InflaterFactory getInflaterFactory()
      Get the InflaterFactory used for these options. Defaults to BlockGunzipper.getDefaultInflaterFactory().
      Returns:
      the InflaterFactory used for these options

    • setInflaterFactory

      public BAMDecoderOptions setInflaterFactory(InflaterFactory inflaterFactory)
      Set the InflaterFactory to use for these options. Defaults value is BlockGunzipper.getDefaultInflaterFactory().
      Parameters:
      inflaterFactory - inflater factory to use
      Returns:
      updated BAMDecoderOptions

    • isAsyncIO

      public boolean isAsyncIO()
      Determine if async IO is enabled for these options. Defaults to Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS.
      Returns:
      true if async IO is enabled for these options

    • setAsyncIO

      public BAMDecoderOptions setAsyncIO(boolean asyncIO)
      Set whether async IO is enable for these options. Defaults value is Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS.
      Parameters:
      asyncIO - true if async IO should be used, otherwise false
      Returns:
      updated BAMDecoderOptions

    • isValidateCRCChecksums

      public boolean isValidateCRCChecksums()
      Determine whether validation of CRC checksums is enabled for these options. Defaults to false.
      Returns:
      true if CRC validation is enabled, otherwise false

    • setValidateCRCChecksums

      public BAMDecoderOptions setValidateCRCChecksums(boolean validateCRCChecksums)
      Set whether validation of CRC checksums should be enabled for these options. Defaults value is false.
      Parameters:
      validateCRCChecksums - true to enable CRC validation, otherwise false
      Returns:
      updated BAMDecoderOptions