[dependabot]

Bumps the cargo-patch-minor group with 5 updates in the / directory:

Package	From	To
clap	4.6.6	4.6.7
flate2	1.1.9	1.1.10
gzp	2.0.2	2.0.4
log	0.4.33	0.4.34
fastqc-rust	1.0.1	1.1.0

Updates clap from 4.6.6 to 4.6.7

Release notes

Sourced from clap's releases.

v4.6.7

[4.6.7] - 2026-09-14

Features

• (derive) Add #[command(defer = <bool>)] attribute to opt-in to lazy initialisation of subcommands

Changelog

Sourced from clap's changelog.

[4.6.7] - 2026-09-14

Features

• (derive) Add #[command(defer = <bool>)] attribute to opt-in to lazy initialisation of subcommands

Commits

• d3e59a9 chore: Release
• d997f87 docs: Update changelog
• fb6058c Merge pull request #6409 from heaths/pwsh-support
• 2310870 test(complete): Add tests for completer_for_path
• 5967c17 refactor(complete): Move shell detection to Shells
• 594602b fix(complete): Detect pwsh for PowerShell
• 3a4f2d0 Merge pull request #6427 from clap-rs/renovate/shlex-2.x
• 67ebaed Merge pull request #6426 from clap-rs/renovate/actions-checkout-7.x
• c968b13 chore(deps): Update Rust crate shlex to v2
• 8f247cb chore(deps): Update actions/checkout action to v7
• Additional commits viewable in compare view

Updates flate2 from 1.1.9 to 1.1.10

Release notes

Sourced from flate2's releases.

1.1.10

What's Changed

• feat: reuse zlib's decoder buffer by @​Vaiz in rust-lang/flate2-rs#532
• feat: add reset method for read::GzDecoder and buffered::GzDecoder by @​Vaiz in rust-lang/flate2-rs#534
• Drop cloudflare-zlib by @​kornelski in rust-lang/flate2-rs#539
• Add a wrapper for the Crc struct by @​MikkelPaulson in rust-lang/flate2-rs#540
• Bump miniz_oxide to 0.9 by @​oscargus in rust-lang/flate2-rs#543
• Upgrade miniz_oxide and add unit tests of the different flush kinds by @​fintelia in rust-lang/flate2-rs#498
• Fix infinite loop in writing gzip header/footer by @​Shnatsel in rust-lang/flate2-rs#547
• test: generate corrupt gzip fixture at runtime by @​nanookclaw in rust-lang/flate2-rs#550
• Reject oversized gzip extra fields by @​Byron in rust-lang/flate2-rs#553
• Reject incomplete deflate streams at EOF by @​Guflly in rust-lang/flate2-rs#556
• Include README.md in a private module by @​bushrat011899 in rust-lang/flate2-rs#562
• Add no_std support using nightly alloc_io by @​bushrat011899 in rust-lang/flate2-rs#559
• Update get_mut() documentation to make clear how 'inner` can be used by @​Byron in rust-lang/flate2-rs#558

New Contributors

• @​Vaiz made their first contribution in rust-lang/flate2-rs#532
• @​MikkelPaulson made their first contribution in rust-lang/flate2-rs#540
• @​oscargus made their first contribution in rust-lang/flate2-rs#543
• @​nanookclaw made their first contribution in rust-lang/flate2-rs#550
• @​Guflly made their first contribution in rust-lang/flate2-rs#556
• @​bushrat011899 made their first contribution in rust-lang/flate2-rs#562

Full Changelog: rust-lang/flate2-rs@1.1.9...1.1.10

Commits

• ed93d4f Merge pull request #558 from rust-lang/lib-doc-update
• fb5228d Merge pull request #559 from bushrat011899/no_std
• 6ed3ba3 Add executable no_std example
• faed8a0 Expand CI to test no_std compatibility and correctness
• 2ba8e7e Add unstable no_std support behind flate2_unstable_nightly_alloc_io
• 3fe1126 Centralize usage of std for error and io
• 98e313a Add GzHeader::mtime_as_duration
• 0642965 Switch to core implicit prelude and only use std where required
• 454a63c Remove left-over dbg! statement
• 2a490b7 Add runtime_detection feature
• Additional commits viewable in compare view

Updates gzp from 2.0.2 to 2.0.4

Changelog

Sourced from gzp's changelog.

v2.0.4

• chore: Refresh bytes, thiserror, libdeflater, proptest, and tempfile, and move the lockfile off the yanked spin 0.9.8 release.
• chore: Update the pinned actions/checkout workflow action to v7.0.1.

v2.0.3

• fix: Prevent ParCompress from attempting teardown twice after an internal writer error, so write, flush, and finish preserve the original error instead of panicking during Drop (#68).
• perf: Keep send-error recovery on the cold error path so successful compression does not pay for teardown handling.

Commits

• cb76904 release: prepare v2.0.4 (#78)
• 6873270 fix: disarm ParCompress after send errors (#70)
• 3f33f06 ci: refresh GitHub Actions setup (#71)
• See full diff in compare view

Updates log from 0.4.33 to 0.4.34

Release notes

Sourced from log's releases.

0.4.34

What's Changed

• doc: Add context-logger utility to README by @​alekseysidorov in rust-lang/log#735
• Add alloc support for boxed loggers by @​malezjaa in rust-lang/log#737

New Contributors

• @​alekseysidorov made their first contribution in rust-lang/log#735
• @​malezjaa made their first contribution in rust-lang/log#737

Full Changelog: rust-lang/log@0.4.33...0.4.34

Changelog

Sourced from log's changelog.

[0.4.34] - 2026-08-22

What's Changed

• doc: Add context-logger utility to README by @​alekseysidorov in rust-lang/log#735
• Add alloc support for boxed loggers by @​malezjaa in rust-lang/log#737

New Contributors

• @​alekseysidorov made their first contribution in rust-lang/log#735
• @​malezjaa made their first contribution in rust-lang/log#737

Full Changelog: rust-lang/log@0.4.33...0.4.34

Commits

• 8034743 Merge pull request #738 from rust-lang/cargo/0.4.34
• 7d1e24e prepare for 0.4.34 release
• 3b939b6 Merge pull request #737 from malezjaa/master
• b88266c Add alloc support for boxed loggers
• 037d7a5 doc: Add context-logger utility to README
• See full diff in compare view

Updates fastqc-rust from 1.0.1 to 1.1.0

Release notes

Sourced from fastqc-rust's releases.

FastQC-Rust v1.1.0

[!NOTE] Tracking: FastQC v0.13.0

Upstream changes (Java FastQC v0.13.0)

Output matches Java FastQC v0.13.0 (#11). Many of its changes came from this project: see upstream contributions.

• Phred+33 is the default; encoding autodetection is gone. Use --phred64 for legacy files.
• Basic Statistics gains Mean Length and Median Length, and drops Sequences flagged as poor quality.
• --min_length now filters reads instead of padding plots. New --max_length does the same for long reads.
• SVG graphs are the default in the HTML report. Use --png for PNG.

FastQC-Rust changes

These are specific to the Rust rewrite.

Performance

• Multi-threaded by default. -t/--threads is now a total budget for the whole run (default: available CPUs, up to 6), so a single .fastq.gz uses several cores. -t 1 keeps everything, gzip decoding included, on one thread. (#7, #8)
• Parallel gzip decompression via rapidgzip. Binaries are now pure Rust and fully static.
• Quicker analysis (#13): about 2x faster than v1.0 on a 7.9 GB WES file and 3x on long reads, with much lower memory on long reads. See the benchmarks.

Output stays byte-identical whatever the thread count.

Live progress display

Per-file progress bars with a live Basic Statistics table replace the Approx N% complete lines (#9). Logs and pipes get plain one-line-per-file output; override with FASTQC_PROGRESS=always|never.

Bug fixes

• BAM/SAM input always uses Phred+33 (#10)
• Sequence Duplication Levels are deterministic and match Java on large inputs (#12)
• Per-base charts widen for long reads and --nogroup, as in Java
• --template no longer uses -t, which clashed with --threads
• Quality characters of 128 or above no longer crash the run

Breaking changes for library users

FastQCConfig::threads is now Option<usize>, FastQCConfig has a new decompress_threads field, and SequenceFileGroup::new takes file openers. The native-zlib feature is gone. See the library docs.

Changelog

Sourced from fastqc-rust's changelog.

v1.1.0

[!NOTE] Tracking: FastQC v0.13.0

Upstream changes (Java FastQC v0.13.0)

Output matches Java FastQC v0.13.0 (#11). Many of its changes came from this project: see upstream contributions.

• Phred+33 is the default; encoding autodetection is gone. Use --phred64 for legacy files.
• Basic Statistics gains Mean Length and Median Length, and drops Sequences flagged as poor quality.
• --min_length now filters reads instead of padding plots. New --max_length does the same for long reads.
• SVG graphs are the default in the HTML report. Use --png for PNG.

FastQC-Rust changes

These are specific to the Rust rewrite.

Performance

• Multi-threaded by default. -t/--threads is now a total budget for the whole run (default: available CPUs, up to 6), so a single .fastq.gz uses several cores. -t 1 keeps everything, gzip decoding included, on one thread. (#7, #8)
• Parallel gzip decompression via rapidgzip. Binaries are now pure Rust and fully static.
• Quicker analysis (#13): about 2x faster than v1.0 on a 7.9 GB WES file and 3x on long reads, with much lower memory on long reads. See the benchmarks.

Output stays byte-identical whatever the thread count.

Live progress display

Per-file progress bars with a live Basic Statistics table replace the Approx N% complete lines (#9). Logs and pipes get plain one-line-per-file output; override with FASTQC_PROGRESS=always|never.

Bug fixes

• BAM/SAM input always uses Phred+33 (#10)
• Sequence Duplication Levels are deterministic and match Java on large inputs (#12)
• Per-base charts widen for long reads and --nogroup, as in Java
• --template no longer uses -t, which clashed with --threads
• Quality characters of 128 or above no longer crash the run

Breaking changes for library users

FastQCConfig::threads is now Option<usize>, FastQCConfig has a new decompress_threads field, and SequenceFileGroup::new takes file openers. The native-zlib feature is gone. See the library docs.

Commits

• 4ec9263 Group v1.1.0 changelog into upstream and Rust rewrite changes
• 08bfb60 Shorten v1.1.0 changelog and fix release notes extraction
• 0b497e0 Merge pull request #7 from ewels/claude/rapidgzip-fastqc-rust-dn4k88
• 41be349 Fix gzip progress race with the decoder's byte counter
• 0c0fd31 Fix final review findings for v1.1.0
• 3df20d7 Fix horizontal scroll on the docs site at phone width
• 4f2eae1 Use v-prefixed versions in docs
• 663cf8c Bump version to v1.1.0 and align docs
• 1342b39 Reject -t 0 with an error
• 02a533c Fix code review findings and concatenated-gzip progress
• Additional commits viewable in compare view

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[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.