parallel multi-file VCF ingest, SIMD genotype parsing#83
Merged
Conversation
This was referenced Apr 12, 2026
vineetver
force-pushed
the
perf/simd-vcf-ingest
branch
from
58a86f7 to
b73670f
Compare
Process multiple VCF files concurrently via rayon. Each file gets its
own worker with independent BGZF reader, per-chrom parquet writers, and
optional genotype writer. Workers write part_{id}.parquet per chromosome,
scan_and_register merges metadata after all workers join.
23 UKB chr22 blocks (163GB BGZF, 414K variants, 200K samples):
sequential extrapolation: ~97 min
parallel (16 cores, 64G): 9m28s — 10x speedup, 68% CPU efficiency
Also: memchr SIMD for genotype tab scanning (41% single-file speedup),
RecordContext replaces 15-parameter process_record, dedup ascii_uppercase_into,
validate sample consistency across files before spawning workers,
Output trait is Send+Sync for thread safety.
vineetver
force-pushed
the
perf/simd-vcf-ingest
branch
from
b73670f to
93ac488
Compare
This was referenced Apr 12, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Benchmarks (UKB chr22, 200K samples, 16 cores, 64G)
Sequential extrapolation for 23 blocks: ~97 min. Parallel: 7m03s. 14x speedup.
Test plan
cargo test-- 270 tests passPartially addresses #74.