Skip to content

osteosarc 0.12.0

Choose a tag to compare

@iskandr iskandr released this 26 Sep 18:10
· 21 commits to main since this release
03af4a3

Test data in a call or two (#73).

  • Make a bundle without a recipe. osteosarc test-data make DIR SAMPLE|FILE --variant ID --sv ID and data.make_bundle(dir, variants=..., files=...) write a
    verified bundle with openvax-v1's selection: a balanced set of templates at each
    variant in each BAM, and templates joining each SV's breakends, every record pinned.
    Files can be BAMs or samples. They say which BAMs they skip and why, and stop,
    before streaming any reads, if a requested variant or SV can't be read from the BAMs
    given. test-data make DIR --recipe FILE replaces test-data generate, and fetches
    the recipe's sources from the snapshot it names, so a bundle's own recipe.json
    rebuilds it.
  • Use a member in one call. osteosarc.bundle_file(bundle, member) returns it as a
    local indexed BAM (or SAM), exported once into the cache with the other members from
    its source BAM, read-only, and reused offline: the helper each OpenVax library had
    written for itself. An unknown member's error suggests close names.
  • One rule for bundles. list_bundle, export_bundle, verify_bundle, check_fixtures
    and bundle_file all take a bundle folder or a published bundle's bare name, such as
    openvax-v1; a Path, or text with a slash, is always a folder. Offline, a bundle that
    isn't cached yet says how to get it.
  • The package docstring, the data overview, osteosarc --help and the docs lead
    with these.