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osteosarc 0.11.0

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@iskandr iskandr released this 26 Sep 06:20
· 25 commits to main since this release
1ca5c1b

The OpenVax libraries can take their test reads from one place: openvax-v1, chosen
once here (#56). See
shared test data.

  • What it holds: reads at every variant on the site plus other alleles the
    libraries test, reads joining the breakends of 7 RNA fusions and 8 DNA SVs, and
    every record in Isovar's, Topiary's, Vaxrank's and Varcode's current test files,
    exactly as they are.
  • Using it: osteosarc test-data list openvax-v1 downloads it the first time, and
    export and verify take its name too; check compares a library's own copies with
    it. In Python, fetch_bundle("openvax-v1") returns its folder.
  • How reads are chosen: a new allele classifier sorts each read at a variant into
    alt, ref, other or uncallable, even for indels in repeats, and openvax-v1 keeps up
    to 20 alt, 10 ref, 5 other and 2 uncallable templates per variant and BAM, whole.
  • Export writes just the members. osteosarc test-data export BUNDLE DIR --member NAME writes NAME.bam, with its index, into DIR, which may already exist; it no
    longer copies the whole bundle, and never replaces a different file. Manifests no
    longer record exports.
  • Recipes: an exact member can give each record its own reason, and a target can
    be one of a library's test files.
  • Docs: the example file names for reads saved with --to now match what it writes.