Class CRAMCodecModelContext

java.lang.Object
htsjdk.samtools.cram.structure.CRAMCodecModelContext
public class CRAMCodecModelContext extends Object
Context model data for use by CRAM 3.1 codec write implementations that need per-record metadata beyond the raw byte stream. Populated during slice construction from the list of CRAM records, then passed through to ExternalCompressor.compress(byte[], CRAMCodecModelContext) calls. Currently used by FQZComp, which needs per-record quality score lengths and BAM flags to properly compress quality scores with context modeling.

  • Constructor Details

    • CRAMCodecModelContext

      public CRAMCodecModelContext()

  • Method Details

    • populateFromRecords

      public void populateFromRecords(List<CRAMCompressionRecord> records)
      Populate this context from the records in a slice. Should be called during slice construction before records are written to blocks.
      Parameters:
      records - the CRAM records for this slice

    • getQualityScoreLengths

      public int[] getQualityScoreLengths()
      Returns:
      per-record quality score lengths (one per record in the slice), or null if not populated

    • getBamFlags

      public int[] getBamFlags()
      Returns:
      per-record BAM flags (one per record in the slice), or null if not populated

    • getNumRecords

      public int getNumRecords()
      Returns:
      number of records, or 0 if not populated