julius-muller/vcfcache: vcfcache v0.4.0

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Authors: Julius Müller
Cited by: 0

Abstract

v0.4.0 (2026-01-05) Added Added detailed timing breakdown to blueprint-init, blueprint-extend, cache-build, and annotate commands when --debug flag is provided (similar to demo --smoke-test output) Added comprehensive performance model documentation to WIKI.md explaining runtime efficiency, cache lookup mechanics, and expected speed-ups (2-10× for typical samples with 60-90% cache hits) Added brief performance summary to README.md with link to detailed model Added caveat section explaining when caching provides less benefit (small datasets, fast pipelines) Added troubleshooting note about VEP non-deterministic output in recent versions (ensembl-vep#1959) Changed Simplified list command interface: Removed vcfcache caches and vcfcache blueprints convenience aliases (use vcfcache list caches and vcfcache list blueprints instead) Made selector (blueprints/caches) a required positional argument Simplified options: --local [PATH] now optionally takes a path directly Improved demo command help text to clearly distinguish smoke test mode vs benchmark mode vcfcache demo and vcfcache list now show compressed help when run without required arguments (full help available with --help) Updated all documentation to reflect new CLI interface and performance model

Publication details

Journal / source
Zenodo (CERN European Organization for Nuclear Research)
Publication date
5 January 2026