[OC-833b] parallelize oc util mergesqlite - #422
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Adds `--parallel`/`--workers N` to `oc util mergesqlite`: shards the structural merge and postaggregator recompute by chromosome (ProcessPoolExecutor), then concatenates shards and renumbers uids globally. Gene table is merged once, globally, instead of per shard. casecontrol is not supported in --parallel mode (hard error if it would otherwise run); vcfinfo's multi_sample now comes from vcfinfo's own --confs override instead of a monkeypatch.
Previously, chromosomes were divided one bucket per processor, and each processor was pre-assigned a bucket. Unequal buckets led to inefficient work division and longer wall-time runs. Now, there's a work queue were each job is one chromosome, leading to more efficient division of work. Additionaly, the serial writing of chromosomes into the final file begins as soon as the first chromosome is finished, leading to an earlier start to the long serial process, and a far quicker finish to the overall process.
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August 29, 2026 04:48
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Optional PR adding a parallel implementation of
oc util mergsqlite, by partitioning the merge on chromosomes. In testing, this improved performance ~2x with 4 CPUs available. The postaggregator step still runs single threaded, but variant merging happens much faster.This PR is dependent upon a change in the vcfinfo module here: KarchinLab/open-cravat-modules-karchinlab#66