Class FQZCompEncode

java.lang.Object
htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
public class FQZCompEncode extends Object
Encoder for the CRAM 3.1 FQZComp quality score compression codec. Uses an adaptive arithmetic (range) coder with a 16-bit context model built from quality history, position within read, and optionally delta and selector information.

The encoder analyzes quality data to select context model parameters, matching the adaptive parameter training in htslib's fqz_pick_parameters (fqzcomp_qual.c). Features:

  • Quality map for sparse symbol sets (e.g., NovaSeq 4-bin quality)
  • Delta table with approximate-sqrt mapping for running quality difference context
  • Symbol-count-based tuning (NovaSeq, HiSeqX, small datasets)
  • Duplicate detection for consecutive identical quality strings
  • Quality reversal for reverse-complemented reads (GFLAG_DO_REV)
  • Fixed-length read optimization
See Also:

  • Constructor Details

    • FQZCompEncode

      public FQZCompEncode()

  • Method Details

    • compress

      public ByteBuffer compress(ByteBuffer inBuffer, int[] recordLengths)
      Compress concatenated quality scores using the FQZComp codec.
      Parameters:
      inBuffer - concatenated quality scores for all records (position to limit is compressed)
      recordLengths - per-record quality score lengths; sum must equal inBuffer.remaining()
      Returns:
      a rewound ByteBuffer containing the compressed data

    • compress

      public ByteBuffer compress(ByteBuffer inBuffer, int[] recordLengths, int[] bamFlags)
      Compress concatenated quality scores using the FQZComp codec with per-record BAM flags.
      Parameters:
      inBuffer - concatenated quality scores for all records (position to limit is compressed)
      recordLengths - per-record quality score lengths; sum must equal inBuffer.remaining()
      bamFlags - per-record BAM flags (for reverse-complement and dedup detection), or null
      Returns:
      a rewound ByteBuffer containing the compressed data

    • storeArray

      public static void storeArray(ByteBuffer outBuffer, int[] array, int size)
      Serialize an array using the two-level run-length encoding used by FQZComp for tables. This is the inverse of FQZUtils.readArray(ByteBuffer, int[], int).
      Parameters:
      outBuffer - output buffer to write to
      array - the array to serialize
      size - number of elements to serialize