Class FQZCompExternalCompressor

java.lang.Object
htsjdk.samtools.cram.compression.ExternalCompressor
htsjdk.samtools.cram.compression.fqzcomp.FQZCompExternalCompressor
public class FQZCompExternalCompressor extends ExternalCompressor
External compressor wrapper for the FQZComp quality score codec. Bridges the ExternalCompressor interface with the FQZComp encoder/decoder, extracting per-record metadata from the CRAMCodecModelContext that the encoder needs to determine record boundaries.

  • Constructor Details

  • Method Details

    • compress

      public byte[] compress(byte[] data, CRAMCodecModelContext contextModel)
      Compress quality score data using FQZComp. Per-record quality score lengths are extracted from the context model; if unavailable or mismatched, the data is treated as a single record. Empty data is returned as-is.
      Specified by:
      compress in class ExternalCompressor
      Parameters:
      data - concatenated quality scores
      contextModel - context containing per-record lengths and flags, or null
      Returns:
      compressed data

    • uncompress

      public byte[] uncompress(byte[] data)
      Decompress the data.
      Specified by:
      uncompress in class ExternalCompressor
      Parameters:
      data - the compressed data
      Returns:
      the decompressed data