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osteosarc 0.11.0
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-v1downloads 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 NAMEwrites 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.