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supersedes/closes #99, #129, #130, #131 with no duplicate dep - #140

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deps-bump
Jul 28, 2026
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supersedes/closes #99, #129, #130, #131 with no duplicate dep#140
Psy-Fer merged 1 commit into
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deps-bump

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@Psy-Fer Psy-Fer commented Jul 28, 2026

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deps: bump log / env_logger / bstr / noodles, and dedupe noodles-bgzf

Consolidates the four Rust-dependency dependabot bumps into one verified PR, plus the follow-up dependabot's noodles bump needs but doesn't include (deduping noodles-bgzf).

Supersedes / closes #99, #129, #130, #131.

Bumps

Crate From To
log 0.4.32 0.4.33 patch
env_logger 0.11.10 0.11.11 patch
bstr 1.12.1 1.13.0 minor
noodles 0.111 0.113 minor (pulls noodles-sam 0.85→0.87, noodles-bam 0.90→0.92, noodles-csi 0.56→0.58)
noodles-bgzf 0.47 0.49 dedupe (see below)

Why the extra noodles-bgzf bump

noodles 0.113 depends on noodles-bgzf 0.49 internally, while our direct dep (the BAM writer's libdeflate BGZF path) was pinned to 0.47 — so bumping noodles alone (dependabot #130) leaves two noodles-bgzf versions in the tree (0.47 + 0.49). Bumping our direct dep to 0.49 dedupes to a single version; the libdeflate feature is intact and BAM output is unchanged.

Validation

  • Builds clean; clippy --all-targets 0 warnings; fmt clean.
  • 579 tests pass (unit + integration, including the BAM write/read round-trip tests — the main API-break risk for a noodles minor bump).
  • Single noodles-bgzf version in the dep tree after the dedupe.

@Psy-Fer Psy-Fer self-assigned this Jul 28, 2026
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Psy-Fer enabled auto-merge (squash) July 28, 2026 02:43
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Psy-Fer merged commit 4368294 into main Jul 28, 2026
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Psy-Fer deleted the deps-bump branch July 28, 2026 02:49
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