Split chrPloidy into its own CTE in the CNV gene query - #230
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Pre-filtering the chromosome side and repeating the sample filter on the gene side lets the planner parallelise the GeneCopyNumbers scan: bySample drops from 7.2s single-threaded to 4.3s on 2 workers. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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What
GeneCopyNumbersByOrganism'sbySampleCTE (Model/lib/wdk/model/questions/queries/geneQueries.xml) joinedGeneCopyNumbersandChrCopyNumbersin one flat comma-join. This splits the chromosome side into its ownchrPloidyCTE and repeats the sample filter on both sides.Why
With the chromosome side pre-filtered, the planner parallelises the
GeneCopyNumbersscan — 2 workers,bySamplemeasured at 4.3s instead of 7.2s single-threaded (~30%).Repeating
eda_sample_stable_id IN (...)on the gene side is what enables it: the gene side gets its own restriction rather than inheriting one through the join. The duplication is deliberate and is called out in a comment so it doesn't get "cleaned up" later.Notes
eda_sample_stable_id,na_sequence_id) and the sameorganismrestriction on both tables, just expressed as an explicitJOINagainst a filtered CTE.ea4272bdc("Add na_sequence_id to the GeneCopyNumbers tuning index"), which is what makes the chromosome-side filter cheap.b4acd8369); clean, no conflicts.Verification
Measurement above was taken when the change was written. The timings predate the rebase, and this has not been re-run against current master or built on an instance — worth a fresh
EXPLAIN ANALYZEbefore merging if the CNV path matters for the release.🤖 Generated with Claude Code