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Cramv4 #502

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Cramv4 #502

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Commits on May 28, 2020

  1. First draft of CRAM v4.0 specification

    This has been forked from CRAMv3.tex c831aba as given this is a major
    release we don't wish to keep markup for both versions in the same
    document.
    jkbonfield committed May 28, 2020
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  2. Further CRAMv4.0 updates

    This includes a massive reorganisation of the document, which is long
    overdue.
    
    It also now replaces EXTERNAL with a variety of type specific codecs
    for signed, unsigned and bytes; ditches HUFFMAN (along with all other
    bit codecs) and adds CONST codecs instead; removes the CORE block;
    removes "external" for block descriptions, instead favouring data
    blocks as a way to distinguish from header / structure containing
    blocks.
    
    As yet, nothing implements this variant of V4.0! However it's far
    cleaner to describe and hopefully far simpler to implement due to
    the aggressive culling of largely unused features.
    jkbonfield committed May 28, 2020
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  3. More CRAM 4 shuffling

    - BYTE is now the same ID as the old EXTERNAL, given it's identical.
      But we refer to it as BYTE for clarity sake.
    
    - Removed sint vs uint in data series types as it's no longer
      necessary to bake this into the specification.
    
    - Moved the Data Series format text to later on and merged with the
      other tables, so the concepts and formats are introduced at the same
      point.
    jkbonfield committed May 28, 2020
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  5. Minor table layout change

    jkbonfield committed May 28, 2020
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Commits on Jun 22, 2020

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Commits on Jan 29, 2024

  1. Document FP is delta against the last FP or zero.

    See samtools#747 for CRAM 3.x issue.
    jkbonfield committed Jan 29, 2024
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