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varfish-org / mehari

VEP-like tool for sequence ontology and HGVS annotation of VCF files
MIT License
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build(deps): bump the noodles group across 1 directory with 8 updates #454

Closed dependabot[bot] closed 3 months ago

dependabot[bot] commented 4 months ago

Bumps the noodles group with 8 updates in the / directory:

Package From To
annonars 0.36.1 0.36.2
noodles-bgzf 0.26.0 0.29.0
noodles-core 0.14.0 0.15.0
noodles-csi 0.30.0 0.33.0
noodles-fasta 0.33.0 0.39.0
noodles-tabix 0.36.0 0.39.0
noodles-vcf 0.49.0 0.55.0
seqrepo 0.10.0 0.10.1

Updates annonars from 0.36.1 to 0.36.2

Release notes

Sourced from annonars's releases.

v0.36.2

0.36.2 (2024-05-08)

Bug Fixes

Changelog

Sourced from annonars's changelog.

0.36.2 (2024-05-08)

Bug Fixes

Commits
  • bb6166f chore(main): release 0.36.2 (#448)
  • 683c84d fix: update noodles group (#447)
  • 41512ca build(deps): bump serde_json from 1.0.113 to 1.0.114 (#429)
  • 6dee8ee build(deps): bump serde from 1.0.196 to 1.0.197 (#428)
  • 1a015ee build(deps): bump insta from 1.34.0 to 1.36.1 (#427)
  • 0204473 build(deps): bump test-log from 0.2.14 to 0.2.15 (#426)
  • 276c15a build(deps): bump anyhow from 1.0.79 to 1.0.80 (#425)
  • c927a68 build(deps): bump actions/add-to-project from 0.5.0 to 0.6.0 (#424)
  • 2ce7622 build(deps): bump GoogleCloudPlatform/release-please-action from 3 to 4 (#410)
  • See full diff in compare view


Updates noodles-bgzf from 0.26.0 to 0.29.0

Commits
  • fa13443 Bump versions for noodles 0.71.0
  • 6718e0a bgzf/changelog: Fix typo
  • 12680ba vcf/async/io/reader: Remove Reader::virtual_position
  • a3b8e35 bam/async/io/reader: Remove Reader::virtual_position
  • fb54e41 bcf/io/reader: Remove Reader::seek
  • bb723bd bcf/io/reader: Remove Reader::virtual_position
  • 63c9dad cram/codecs/name_tokenizer/decode: Fix clippy::assigning_clones warnings
  • 9488891 bcf/record/samples/series: Remove stray dbgs
  • b15e790 bgzf/multithreaded_reader: Directly copy from the block buffer when the given...
  • 5bc27fe bgzf/multithreaded_reader: Remove MultithreadedReader::seek
  • Additional commits viewable in compare view


Updates noodles-core from 0.14.0 to 0.15.0

Commits
  • 58e6bc6 Bump versions for noodles 0.72.0
  • 4f7f32a vcf/changelog: Fix section title
  • 01110b0 vcf/io/writer/header/record: Write newlines for records in other collections
  • e4a45d1 vcf/io/writer/header/record/value/map: Move number writer to info module
  • c16ac23 vcf/header/parser/record/value/map/info: Add number parser
  • 6bdbf75 vcf/header/parser/record/value/map/format: Add number parser
  • c7fd2b0 vcf/io/writer/header/record/value/map/format: Add number writer
  • 50ab168 vcf/header/record/value/map: Add associated number type to Typed
  • 53cea57 vcf/header/number: Expand variant names
  • f7f2431 bgzf/multithreaded_reader/tests: Fix typo
  • Additional commits viewable in compare view


Updates noodles-csi from 0.30.0 to 0.33.0

Commits
  • fa13443 Bump versions for noodles 0.71.0
  • 6718e0a bgzf/changelog: Fix typo
  • 12680ba vcf/async/io/reader: Remove Reader::virtual_position
  • a3b8e35 bam/async/io/reader: Remove Reader::virtual_position
  • fb54e41 bcf/io/reader: Remove Reader::seek
  • bb723bd bcf/io/reader: Remove Reader::virtual_position
  • 63c9dad cram/codecs/name_tokenizer/decode: Fix clippy::assigning_clones warnings
  • 9488891 bcf/record/samples/series: Remove stray dbgs
  • b15e790 bgzf/multithreaded_reader: Directly copy from the block buffer when the given...
  • 5bc27fe bgzf/multithreaded_reader: Remove MultithreadedReader::seek
  • Additional commits viewable in compare view


Updates noodles-fasta from 0.33.0 to 0.39.0

Commits
  • 906f523 Bump versions for noodles 0.75.0
  • 3c5713d vcf/header/parser/record/value: Match error message map identifier format
  • 970bbca vcf/io/writer/header/record/value: Validate unstructured header record value
  • 3727fff fasta/io/writer/record/sequence: Use newline writer
  • d06b3da fasta/io/writer/record: Rename newline constant
  • 07d8422 vcf/io/writer/record/position: Inline format argument
  • 80a89b8 bcf/record/codec/decoder/samples/values: Handle missing string array values
  • 287027b bcf/record/codec/decoder/samples/values: Handle missing string values
  • a0ac6f9 vcf/changelog: Fix typo
  • 4ed0117 vcf/async/io/reader/header: Parse header line by line
  • Additional commits viewable in compare view


Updates noodles-tabix from 0.36.0 to 0.39.0

Commits
  • fa13443 Bump versions for noodles 0.71.0
  • 6718e0a bgzf/changelog: Fix typo
  • 12680ba vcf/async/io/reader: Remove Reader::virtual_position
  • a3b8e35 bam/async/io/reader: Remove Reader::virtual_position
  • fb54e41 bcf/io/reader: Remove Reader::seek
  • bb723bd bcf/io/reader: Remove Reader::virtual_position
  • 63c9dad cram/codecs/name_tokenizer/decode: Fix clippy::assigning_clones warnings
  • 9488891 bcf/record/samples/series: Remove stray dbgs
  • b15e790 bgzf/multithreaded_reader: Directly copy from the block buffer when the given...
  • 5bc27fe bgzf/multithreaded_reader: Remove MultithreadedReader::seek
  • Additional commits viewable in compare view


Updates noodles-vcf from 0.49.0 to 0.55.0

Commits
  • fa13443 Bump versions for noodles 0.71.0
  • 6718e0a bgzf/changelog: Fix typo
  • 12680ba vcf/async/io/reader: Remove Reader::virtual_position
  • a3b8e35 bam/async/io/reader: Remove Reader::virtual_position
  • fb54e41 bcf/io/reader: Remove Reader::seek
  • bb723bd bcf/io/reader: Remove Reader::virtual_position
  • 63c9dad cram/codecs/name_tokenizer/decode: Fix clippy::assigning_clones warnings
  • 9488891 bcf/record/samples/series: Remove stray dbgs
  • b15e790 bgzf/multithreaded_reader: Directly copy from the block buffer when the given...
  • 5bc27fe bgzf/multithreaded_reader: Remove MultithreadedReader::seek
  • Additional commits viewable in compare view


Updates seqrepo from 0.10.0 to 0.10.1

Release notes

Sourced from seqrepo's releases.

v0.10.1

0.10.1 (2024-03-07)

Bug Fixes

Changelog

Sourced from seqrepo's changelog.

0.10.1 (2024-03-07)

Bug Fixes

Commits
  • aada2fe chore(main): release 0.10.1 (#101)
  • 6d6c1e2 build(deps): bump the noodles group with 1 update (#97)
  • 1e0974c build(deps): update rusqlite requirement from 0.30 to 0.31 (#96)
  • 4b6e531 build(deps): bump actions/add-to-project from 0.5.0 to 0.6.0 (#98)
  • 19eb0d6 fix: use column for seqid alias query (#100)
  • See full diff in compare view


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dependabot[bot] commented 3 months ago

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