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vflank 0.4.0

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@rhshah rhshah released this 15 Jun 12:49
· 19 commits to main since this release
v0.4.0
a0f0104

Highlights

No-download reference via the UCSC API (--ref-source api) — for both small and fusion, fetch each flank window from api.genome.ucsc.edu instead of a local FASTA, so a run needs no multi-GB reference on disk (the prerequisite for hosting vflank as a service). --ref-genome is now optional, required only for the default file backend (clear error otherwise — no silent fallback). The UCSC path uses the same 0-based half-open coordinates as the local one (flank math unchanged), throttles to ~1 req/s, caches per window, retries transient failures, and reports a reference-API request count.

Use a local FASTA (--ref-source file, default) for bulk/offline/HPC runs; the API backend is best for hosted single-variant / small use.

Also

  • --help for small/fusion groups options into labelled panels.
  • New Recommended Usage page, reference-API and web-app/hosting design notes, and PyPI/GHCR/DeepWiki badges.

See the changelog for details.

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