Profile the VEP annotation pipeline end-to-end and present a structured timing breakdown (pipeline stages, Lance variation/SIFT lookup, engine + transcript-engine stages) to find bottlenecks. Use this whenever the user wants to profile, benchmark, or get a performance/timing breakdown of vepyr annotation, the variation cache lookup, the VEP engine, or asks "where is the time going / what's the bottleneck" for chr-scale annotation — even if they don't say the word "profile". Also use after a cache-layout or encoding change to confirm lookup cost and that the pipeline is still engine-bound.
2026-07-01