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CRISPRme+ 2.2.0-alpha.13

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@lucapinello lucapinello released this 14 Aug 18:11
· 49 commits to main since this release
425c743

Alpha release for beta users. Docker: docker pull pinellolab/crisprme:v2.2.0-alpha.13 (multi-arch amd64 + arm64)

Performance follow-up to alpha.12's genome-wide post-analysis memory fix (no behavior change):

Changed

  • ijson now uses the fast yajl2_cffi C backend (added yajl + cffi) instead of the
    pure-python fallback — much faster streaming of the per-chromosome SNP dictionary.
  • Post-analysis runs chromosomes in parallel again. With streaming, per-worker peak RAM is
    small (chromosome genome string + queried subset), so the worker cap uses a modest fixed
    estimate when ijson is available instead of sizing from the (large) dictionary file — which
    had been serializing to a single worker. The INDEL pool likewise (it reads the small
    log_indels, never the big dictionary).

(alpha.12 remains the crash-fix release: genome-wide variant post-analysis OOM + the on-demand
INDELS double-prefix regression. alpha.13 only makes that post-analysis fast.)