bihealth/hgvs-rs issues and pull requests

#150 - chore(deps): update env_logger requirement from 0.10 to 0.11

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#149 - chore(main): release 0.14.1

Pull Request - State: closed - Opened by varfish-bot about 1 year ago - 1 comment
Labels: autorelease: tagged

#148 - fix: allow import of BioType guide_RNA

Pull Request - State: closed - Opened by holtgrewe about 1 year ago

#147 - chore(main): release 0.14.0

Pull Request - State: closed - Opened by varfish-bot about 1 year ago - 2 comments
Labels: autorelease: tagged

#146 - feat: adding support for selenoproteins (#145)

Pull Request - State: closed - Opened by holtgrewe about 1 year ago - 1 comment

#145 - Add support for selenoproteins

Issue - State: closed - Opened by holtgrewe about 1 year ago
Labels: enhancement

#144 - chore(deps): bump the noodles group with 1 update

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#143 - Address stop codon recoding / stop codon readthrough (SCR)

Issue - State: open - Opened by holtgrewe over 1 year ago - 1 comment
Labels: enhancement

#142 - chore(main): release 0.13.2

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 2 comments
Labels: autorelease: tagged

#141 - fix: add more biotypes from cdot JSON for vep110 release

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#140 - chore: extending extract_gene.py for multiple HGNC IDs

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#139 - chore(main): release 0.13.1

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 1 comment
Labels: autorelease: tagged

#138 - fix: adding back missing Gene::biotype member

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#137 - chore(main): release 0.13.0

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 1 comment
Labels: autorelease: tagged

#136 - feat: make compatible with cdot v0.2.21

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#135 - feat: move out assemblies to biocommons_bioutils crate (#134)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#134 - Switch to using biocommons-bioutils-rs crate for assembly info

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#133 - chore(main): release 0.12.0

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 2 comments
Labels: autorelease: tagged

#132 - fix: problem with annotating stop_retained insertions (#131)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#131 - byte index out of bounds for GRCh37:10:5139789:A:AGTG

Issue - State: closed - Opened by holtgrewe over 1 year ago - 3 comments
Labels: bug

#130 - Allow predictions even for transcripts that have more than one stop codon

Issue - State: open - Opened by holtgrewe over 1 year ago - 1 comment
Labels: enhancement

#129 - chore(main): release 0.11.0

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 1 comment
Labels: autorelease: tagged

#128 - feat: various dependency updates, bump version to 0.11.0

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#127 - chore(deps): update quick_cache requirement from 0.3 to 0.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#126 - Support representing repeated sequences from varnomen

Issue - State: open - Opened by holtgrewe over 1 year ago
Labels: enhancement

#125 - chore: adding templates for issues and pull requests

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#124 - chore(deps): update rstest requirement from 0.17 to 0.18

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#123 - chore(deps): bump the noodles group with 1 update

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#122 - Use features to opt-in into sqlite3 and libpostgres dependencies

Issue - State: open - Opened by holtgrewe over 1 year ago
Labels: enhancement

#121 - ci: set release-please token for varfish-bot

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#120 - chore(main): release 0.10.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#119 - fix: properly configure dependabot for noodles

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#118 - chore(main): release 0.10.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#117 - chore(deps): update indexmap requirement from 1.9.3 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#116 - chore(main): release 0.9.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#115 - feat: express existing thread safety (as most things are immutable)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#114 - feat: more thread safe behaviour with Arc

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#113 - chore(main): release 0.8.2

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#112 - refactor: replace linked-hash-map by indexmap (#111)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#111 - Move away from linked-hash-map

Issue - State: closed - Opened by holtgrewe over 1 year ago

#110 - chore(deps): update criterion requirement from 0.4 to 0.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#109 - chore(main): release 0.8.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#108 - fix: bump dependencies

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#107 - chore(main): release 0.8.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#106 - feat: losen dependencies

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#105 - chore(deps): update quick_cache requirement from 0.2.2 to 0.3.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#104 - chore(main): release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#103 - feat: proper error handling with enums and thiserror (#69)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#102 - ci: use --squash for dependabot automerges

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#101 - chore(main): release 0.6.2

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#100 - fix: issue with non-dup insertion at start of protein (#99)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#99 - Crash on GRCh37:1:89449508:A:ATTTTTTTTTTTT

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#98 - chore(deps): update criterion requirement from 0.3 to 0.4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#97 - build: adding rust-version=1.64.0 to Cargo.toml

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#96 - fix: problem with variants in multi-stop codon txs (#95)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#95 - Problem with annotating p.Met1? variants

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#94 - fix: out of bounds issue on 5'-to-3' shifting beyond CDS

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#93 - fix: out of bounds issue for protein sequence creation

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#92 - fix: only warn on combining RefAlt with whole gene deletion

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#91 - fix: out of bound panic in case of long deletions

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#90 - chore(main): release 0.6.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#89 - fix: cases where dup/inv goes beyond CDS

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#88 - chore(main): release 0.6.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#87 - feat: make some tables visible in `hgvs::sequences`

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#86 - chore(main): release 0.5.2

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#85 - perf: further speeding up translate_cds code (#83)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#84 - Switch from lazy_static to once_cell

Issue - State: open - Opened by holtgrewe almost 2 years ago

#83 - Further tune translate_cds code

Issue - State: closed - Opened by holtgrewe almost 2 years ago - 3 comments

#82 - chore(main): release 0.5.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#81 - perf: tune translate_cds implementation (#80)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#80 - Tune translate_cds implementation

Issue - State: closed - Opened by holtgrewe almost 2 years ago - 5 comments

#79 - Add dependabot automerge Github action

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#78 - chore: add Zenodo badge to README

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#77 - chore(deps): update rstest requirement from 0.16.0 to 0.17.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#76 - chore: create dependabot.yaml file

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#75 - chore: bump seqrepo dependency

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#74 - chore: add badges to README

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#73 - feat: replacing usages of unwrap() with expect or Result (#70)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#72 - fix: case of missing stop codon (in particular ENSEMBL)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#71 - fix: return error if problem in normalization

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#70 - Replace all usages of unwrap

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#69 - Add proper error handling with enum

Issue - State: closed - Opened by holtgrewe almost 2 years ago

#68 - fix: return error in normalization instead of unwrap()

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#67 - fix: issue with transcripts missing stop codon

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#66 - chore(main): release 0.5.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#65 - feat: allow configuring that there is no genome sequence

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#64 - fix: fixing wrong validation assumption about insertions

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#63 - Potentially incorrect prection results

Issue - State: open - Opened by holtgrewe almost 2 years ago

#62 - fix: fixing wrong validation assumption about insertions

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#61 - fix: cases of empty sequence

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#60 - fix: truncate AA insertion at stop codon

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#59 - fix: issue with out of bounds deletion

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#58 - feat: more comprehensive clone for field-less enums

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#57 - fix: remove ref length validation

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#56 - chore: add g_to_n test for cdot json BRCA1

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#55 - fix: fixing projection issues with cdot::json::Provider

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#54 - feat: make sequences module public

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#53 - feat: allow for disabling renormalization

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#52 - feat: improved normalizer configuration

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#51 - chore: make non-adjacent exons error easier to read

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

GitHub / bihealth/hgvs-rs issues and pull requests