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osteosarc 0.12.0
Test data in a call or two (#73).
- Make a bundle without a recipe.
osteosarc test-data make DIR SAMPLE|FILE --variant ID --sv IDanddata.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 FILEreplacestest-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
dataoverview,osteosarc --helpand the docs lead
with these.