Cramv4 #502
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Cramv4 #502
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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.
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.
- 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.
See samtools#747 for CRAM 3.x issue.
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This adds the CRAMv4.tex document. Note this builds on top of CRAMv3.1, but does so only in as far as CRAMv4 includes all the previous codecs and so the TeX doc should be used in conjunction with the CRAMcodecs.tex in #433
For avoidance of conflicts, these two PRs are kept separate. Fortunately this is easy as they change entirely separate filenames (bar Makefile).
A major chunk of this work is a large structural overhaul of the CRAM specification. Reordering, clarification, improved typesetting of some elements (eg see #490 which was backported from here), etc. I didn't particularly want to be making all those changes in two separate documents, but maybe it's worth considering. [An indication of the scale of restructuring is the v3 and v4 tex docs are 2970 and 2689 lines long respectively, but a diff between them is 3255 lines.]
The other work is, obviously, CRAM v4 itself. Hopefully the commits will reflect that.