diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a63f97..eece2d4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/Cargo.lock b/Cargo.lock index 9f77c86..7cdbe63 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -693,9 +693,9 @@ dependencies = [ [[package]] name = "noodles" -version = "0.113.0" +version = "0.115.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "03f0a067d8afc481ba06abe5bd924e89368932d664bea15d671bee3559728421" +checksum = "5ef86cb036ab589c660e76bc6d7741454fe8ff71ba3348f71812936f5c1a43f6" dependencies = [ "noodles-bam", "noodles-bgzf", @@ -705,9 +705,9 @@ dependencies = [ [[package]] name = "noodles-bam" -version = "0.92.0" +version = "0.94.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6e70c87dfebe1800c6a59f1b4fc9e6d69e165876c2d475b2b684862a06225a70" +checksum = "e018289a9da86771349be387224f6634ad56ec48eb16a3a29a7670def5d206c2" dependencies = [ "bstr", "indexmap", @@ -720,9 +720,9 @@ dependencies = [ [[package]] name = "noodles-bgzf" -version = "0.49.0" +version = "0.51.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2ae8e8f7c1fd2e265d79241cea83e6f0ff7da2fa8922b5fe2f3eea8969823b60" +checksum = "280d401d0358893ad706fb6094a18e7f9e8f3002630f4960889cb702b6e2714e" dependencies = [ "bytes", "crossbeam-channel", @@ -742,9 +742,9 @@ dependencies = [ [[package]] name = "noodles-csi" -version = "0.58.0" +version = "0.60.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b522467eb7ae4a226b05182069e895940beda9206a3f4da9dd9395613ec9e5a8" +checksum = "32789eeba9c4001d50de853a4c6a8f0551d586a91d6919c0008dd462231feacb" dependencies = [ "bit-vec", "bstr", @@ -765,9 +765,9 @@ dependencies = [ [[package]] name = "noodles-sam" -version = "0.87.0" +version = "0.89.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "db484fde243408e8713278e6e83dbd67765cbd33612f2383f29b6359059d023f" +checksum = "8063dd9e92825db46ae21813525589d41cff9ce2dcb2a0d25d99af86b274a1c5" dependencies = [ "bitflags", "bstr", diff --git a/Cargo.toml b/Cargo.toml index 8a4638f..eba01fa 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -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 @@ -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"