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This PR adds support for CRAM beta coding.
For more information on beta coding, see the CRAM specification.
The core of this PR is the
BitStreamDecoder
, which is a bit stream decoder. TheBitStreamDecoder
manages two statesbuffer
(the byte value already read) andnbits
(indicating how many bits of thebuffer
are still "alive") and prepares for reading the next bit sequence.The CRAM reader creates a
BitStreamDecoder
based on the core block (the only bit-encoded data block) and shares it between data series that are declared to be beta-encoded (Although the CRAM specification does not explicitly state that a core block may be associated with multiple data series, it seems to be guaranteed by the fact that a test file (1101_BETA.cram
) provided by hts-specs is encoded as such).