chore(deps): bump noodles from 0.111.0 to 0.113.0 - #130
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Bumps [noodles](https://github.com/zaeleus/noodles) from 0.111.0 to 0.113.0. - [Commits](zaeleus/noodles@noodles-0.111.0...noodles-0.113.0) --- updated-dependencies: - dependency-name: noodles dependency-version: 0.113.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
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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.
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Looks like noodles is up-to-date now, so this is no longer needed. |
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Bumps noodles from 0.111.0 to 0.113.0.
Commits
fe2b112Update to noodles 0.113.077aded2bgzf/io/multithreaded_reader: Discard channel disconnection errors when not r...05fdecfbam/record/sequence: Use base count for Sequence::is_empty2b4375bvcf/io/writer/builder: Fix typo9ee7faavcf/record/fields: Initialize default to match RecordBuf40255f6vcf/variant/record_buf/info: Fix typo3475768vcf/variant/record_buf/filters: Require a single PASS filter for passing status548590asam/io/reader/record: Only strip carriage return from CRLF newline8a034cebed/io/reader/record: Only strip carriage return from CRLF newlineaee586cvcf/io/reader/record: Only strip carriage return from CRLF newline