noodles moved fast in the last two weeks and the pins here are two minors behind.
| Crate |
Pinned |
Latest |
Released |
noodles |
0.113 |
0.115.0 |
2026-08-03 |
noodles-bgzf |
0.49 |
0.51.0 |
2026-08-03 |
Pre-1.0, so minors are breaking by convention: this needs reading, not a blind bump.
Why bgzf 0.50 / 0.51 specifically matter here
- 0.50 — multithreaded readers and writers moved off rayon's global pool onto exclusive local
pools, and the deprecated with_worker_count methods came back as the supported way to size them.
- 0.51 — worker count is now synced to the number of managed buffers instead of rayon's global
pool, so merely constructing one no longer initialises that pool.
This codebase leans on rayon for alignment (src/lib.rs and friends). A BGZF component that
quietly borrows the global rayon pool competes with the align workers for the same threads; a
component with its own sized pool does not. That is the interesting part of the upgrade.
The adjacent opportunity
src/io/bam.rs:48 builds a plain single-threaded bgzf::io::Writer for every BAM sink
(:60, :374). BAM output is therefore serialised behind one compressor while alignment runs on N
threads. With 0.50+ the multithreaded writer is usable with an explicit, non-global worker count,
which is exactly the shape needed here.
Caveat that must be checked, not assumed: BGZF block boundaries and therefore output bytes can
depend on the writer's buffering, so a multithreaded writer must be shown to produce a
byte-identical file (or a documented, deliberate change) at every worker count.
Checklist
noodlesmoved fast in the last two weeks and the pins here are two minors behind.noodles0.1130.115.0noodles-bgzf0.490.51.0Pre-1.0, so minors are breaking by convention: this needs reading, not a blind bump.
Why bgzf 0.50 / 0.51 specifically matter here
pools, and the deprecated
with_worker_countmethods came back as the supported way to size them.pool, so merely constructing one no longer initialises that pool.
This codebase leans on rayon for alignment (
src/lib.rsand friends). A BGZF component thatquietly borrows the global rayon pool competes with the align workers for the same threads; a
component with its own sized pool does not. That is the interesting part of the upgrade.
The adjacent opportunity
src/io/bam.rs:48builds a plain single-threadedbgzf::io::Writerfor every BAM sink(
:60,:374). BAM output is therefore serialised behind one compressor while alignment runs on Nthreads. With 0.50+ the multithreaded writer is usable with an explicit, non-global worker count,
which is exactly the shape needed here.
Caveat that must be checked, not assumed: BGZF block boundaries and therefore output bytes can
depend on the writer's buffering, so a multithreaded writer must be shown to produce a
byte-identical file (or a documented, deliberate change) at every worker count.
Checklist
fastq/sam/bam, note breaking changesnoodlesandnoodles-bgzfin separate commits from any behaviour changewith_worker_countbstr1.13,rustc-hash2.1.3,memmap20.9.11 (allcompatible with existing ranges);
dashmap7 is a release candidate, stay on 6