chore(deps): bump noodles 0.113 -> 0.115, noodles-bgzf 0.49 -> 0.51 - #211
Open
BenjaminDEMAILLE wants to merge 1 commit into
Open
chore(deps): bump noodles 0.113 -> 0.115, noodles-bgzf 0.49 -> 0.51#211BenjaminDEMAILLE wants to merge 1 commit into
BenjaminDEMAILLE wants to merge 1 commit into
Conversation
noodles-bgzf 0.50 moves the multithreaded reader/writer off rayon's global thread pool onto exclusive local pools and restores the `with_worker_count` builders; 0.51 syncs the worker count to the number of managed buffers, so constructing one no longer initialises rayon's global pool. That matters here because alignment runs on rayon: a BGZF component borrowing the global pool competes with the align workers. No source change was needed. Verified locally: * `cargo fmt --check`, `cargo clippy --all-targets -- -D warnings` clean * full test suite green (593 tests, 0 failures) * `Aligned.sortedByCoord.out.bam` byte-identical before and after (same sha256 over an identical command line), and the `Genome` / `SA` index bytes unchanged Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Closes #207.
Dependency bump only, no source change.
noodles0.1130.115noodles-bgzf0.490.51Lockfile also moves
noodles-bam0.92 → 0.94,noodles-sam0.87 → 0.89,noodles-csi0.58 → 0.60as transitive consequences.
Why now
The two
noodles-bgzfreleases are about thread-pool ownership, which touches this projectdirectly because alignment runs on rayon:
default global pool, and the previously deprecated
with_worker_countmethods are supportedagain as the way to size them.
rayon's global pool, so constructing one no longer initialises that pool as a side effect.
Today
src/io/bam.rsonly builds single-threadedbgzf::io::Writers, so nothing in this PRdepends on that behaviour. It matters for the follow-up question of whether the BAM writer should
become multithreaded, which is tracked separately in #207 and deliberately not done here.
What was verified
Everything below was run on this branch as submitted.
cargo fmt --check— cleancargo clippy --all-targets -- -D warnings— cleancargo test— 593 tests pass, 0 failures (565 unit + 23 + 4 + 1 across the integration binaries)BAM bytes unchanged. Built the branch, then rebuilt with only
Cargo.toml/Cargo.lockreverted to
origin/main, and ran the identical command against the identical index and outputprefix:
./target/debug/rustar-aligner --runMode genomeGenerate \ --genomeDir /tmp/ab/idx --genomeFastaFiles test/simple.fa --genomeSAindexNbases 4 ./target/debug/rustar-aligner --genomeDir /tmp/ab/idx --readFilesIn test/reads.fq \ --outFileNamePrefix /tmp/ab/run/ --outSAMtype BAM SortedByCoordinate shasum -a 256 /tmp/ab/run/Aligned.sortedByCoord.out.bamSame digest
207b17d3…on both. TheGenomeandSAindex files are likewise identical(
4b09e0e7…/c398a82e…).Note on scope: this uses the bundled
test/simple.fa+test/reads.fqmicro-fixture, so itproves the BGZF/BAM encoding path is unchanged, not that every code path in noodles is. The
--outFileNamePrefixhas to match between the two runs, because the@PG CL:header linerecords the command line and will otherwise differ on its own.
What was not done
No move to the multithreaded BGZF writer, no
with_worker_countplumbing, no behaviour change ofany kind. One theme per PR; the writer question stays in #207.