Class TrialCompressor

java.lang.Object
htsjdk.samtools.cram.compression.ExternalCompressor
htsjdk.samtools.cram.compression.TrialCompressor
public class TrialCompressor extends ExternalCompressor
An ExternalCompressor that tries multiple candidate compressors and selects the one that produces the smallest output. Matches htslib's trial compression approach.

Not thread-safe. Instances must not be shared across threads.

  1. Trial phase (nTrials non-empty blocks): compresses with ALL candidates, picks the smallest for each block, and accumulates sizes to determine the overall winner.
  2. Production phase (next trialSpan blocks): uses the cached winner only.
  3. Re-trial: after trialSpan blocks, re-enters the trial phase to adapt to changing data characteristics.

The compression method is initially null and is set after the first non-empty block is compressed. Calling ExternalCompressor.getMethod() before any non-empty compress(byte[], CRAMCodecModelContext) call will throw IllegalStateException.

See Also:

  • Constructor Details

    • TrialCompressor

      public TrialCompressor(List<ExternalCompressor> candidates)
      Create a trial compressor with the given candidate compressors.
      Parameters:
      candidates - the candidate compressors to try (must have at least 2)

  • Method Details

    • compress

      public byte[] compress(byte[] data, CRAMCodecModelContext contextModel)
      Compress data. During the trial phase, tries all candidates and accumulates size statistics. After nTrials non-empty blocks, selects the overall winner and uses it exclusively until the next re-trial.
      Specified by:
      compress in class ExternalCompressor
      Parameters:
      data - the data to compress
      contextModel - optional codec context model
      Returns:
      the compressed data from the best compressor for this block

    • uncompress

      public byte[] uncompress(byte[] data)
      Decompress data. Delegates to the winner if one has been selected, otherwise to the first candidate. In practice, decompression is handled by the method-specific decompressor selected based on the block's compression method ID, not through this trial compressor.
      Specified by:
      uncompress in class ExternalCompressor
      Parameters:
      data - the compressed data
      Returns:
      the decompressed data