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Staden io_lib 1.14.12
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@jkbonfield jkbonfield released this 31 Jan 17:24
· 58 commits to master since this release
io_lib-1-14-12
e2d8506

This is primarily a change to CRAM, focusing mainly on the unofficial
CRAM 3.1 and 4.0 file formats. Note these newer experimental formats
are INCOMPATIBLE with the 1.14.11 output!

Some changes also affect CRAM 3.0 (current) though. Main updates are:

  • Added compression profiles to scramble: fast, normal (default),
    small and archive. Specify using scramble -X profile-name. These
    change compression codecs permitted as well as the granularity of
    random access ("fast" profile is 1/10th the size per block than
    normal).

  • NM and MD tags are now checked during encode to validate
    auto-generation during decode. If they differ they are stored
    verbatim.

  • CRAM behaves better when many small chromosomes occur in the middle
    of larger ones (as it can switch out of multi-ref mode again).

  • Numerous improvements to CRAM 4.0 compression ratios.

  • Some speed improvements to CRAM 3.1 and 4.0 decoding.

  • Fixes to github issues/bugs #12, #14, #15, #17, #18, #19, #20, #21, #22.

See CHANGES for more details.

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