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osteosarc 0.13.1

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@iskandr iskandr released this 27 Sep 01:32
· 19 commits to main since this release
dd5bd96

Faster commands (#78): three to eight times faster once a snapshot has been used. On the current snapshot:

command before now
reads, on a cached result 7.9 s 2.8 s
files 6.1 s 1.6 s
samples T1_tumor 7.5 s 1.8 s
variants 1.8 s 0.2 s
--version 0.5 s 0.2 s
  • A snapshot's file, header and variant catalogues are saved in the cache the first time, and loaded after.
    • Each user keeps their own copies, which can hold only osteosarc's catalogue classes.
    • A loaded copy warns of stale corrections as a built one does.
  • Files and corrections are found through indexes, not by scanning.
  • pandas is imported only to download a file.

Install: python -m pip install --upgrade osteosarc. No API changes.