Package htsjdk.samtools.cram.compression.nametokenisation

Class NameTokenisationDecode

java.lang.Object
htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
public class NameTokenisationDecode extends Object
CRAM 3.1 NameTokenisation decoder, used to compress read names in CRAM files. The NameTokeniser codec exploits the fact that read names typically follow a structured pattern consisting of alternating alpha and numeric components (i.e., "H0164ALXX140820:2:1101:17727:54981") that can be tokenised and then encoded as one or more differences relative to a previously tokenised name. Uses the rAnsNx16 and/or range codecs internally to compress the resulting token streams.

  • Field Details

  • Constructor Details

    • NameTokenisationDecode

      public NameTokenisationDecode()

  • Method Details

    • uncompress

      public byte[] uncompress(ByteBuffer inBuffer, byte nameSeparator)
      Uncompress the compressed name data in the input buffer. Return is a byte[] containing the read names, each separated by the byte value specified by nameSeparator, including a terminating separator.
      Parameters:
      inBuffer - the buffer to uncompress
      nameSeparator - the name separator byte to use in the output buffer
      Returns:
      the uncompressed read names