Package htsjdk.samtools.cram.encoding.core

Class CoreCodec<T>

java.lang.Object
htsjdk.samtools.cram.encoding.core.CoreCodec<T>
Type Parameters:
T - data series type to be read or written
All Implemented Interfaces:
CRAMCodec<T>
Direct Known Subclasses:
BetaIntegerCodec
public abstract class CoreCodec<T> extends Object implements CRAMCodec<T>
Superclass of Codecs which operate on Core Block bit streams Contrast with htsjdk.samtools.cram.encoding.external.ExternalCodec<T> for External Block byte streams

  • Field Details

    • coreBlockInputStream

      protected final BitInputStream coreBlockInputStream

    • coreBlockOutputStream

      protected final BitOutputStream coreBlockOutputStream

  • Constructor Details

    • CoreCodec

      protected CoreCodec(BitInputStream coreBlockInputStream, BitOutputStream coreBlockOutputStream)
      Create a new CoreCodec with associated input and output bit streams
      Parameters:
      coreBlockInputStream - bit stream for reading input
      coreBlockOutputStream - bit stream for writing output