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chore(deps): bump noodles 0.113 -> 0.115, noodles-bgzf 0.49 -> 0.51 #211

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chore(deps): bump noodles 0.113 -> 0.115, noodles-bgzf 0.49 -> 0.51 #211

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7 changes: 7 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -139,6 +139,13 @@ Sections commonly used: Features, Bug fixes, Other changes.
- `caps-sa` → `0.5` (adds `build_ext_mem_for_filter*`; see the caps-sa
v0.5.0 release notes).

- `noodles` → `0.115`, `noodles-bgzf` → `0.51`. The bgzf releases move
the multithreaded reader/writer off rayon's global thread pool onto
their own local pools, restore the `with_worker_count` builders, and
sync the worker count to the number of managed buffers so that merely
constructing one no longer initialises rayon's global pool. No code
change was needed; BAM output is byte-identical.

### Other

- New module `index::packed_stream` — bit-for-bit-compatible streaming
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20 changes: 10 additions & 10 deletions Cargo.lock
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4 changes: 2 additions & 2 deletions Cargo.toml
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Expand Up @@ -33,7 +33,7 @@ log = "0.4"
env_logger = "0.11"
memmap2 = "0.9"
byteorder = "1"
noodles = { version = "0.113", features = ["fastq", "sam", "bam", "bgzf"] }
noodles = { version = "0.115", features = ["fastq", "sam", "bam", "bgzf"] }
bstr = "1"
# Use the pure-Rust `zlib-rs` backend instead of flate2's default `miniz_oxide`:
# ~2-3x faster inflate/deflate on the FASTQ decode + BGZF (BAM) paths, with no C
Expand Down Expand Up @@ -64,7 +64,7 @@ caps-sa = "0.6"
mimalloc = { version = "0.1", default-features = false }
libmimalloc-sys = { version = "0.1.49", features = ["extended"] } # mi_option_set (purge_delay); see main.rs
libdeflater = "1.25.2"
noodles-bgzf = { version = "0.49", features = ["libdeflate"] }
noodles-bgzf = { version = "0.51", features = ["libdeflate"] }

[dev-dependencies]
assert_cmd = "2"
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