cancervariants/variation-normalization issues and pull requests

#597 - build!: update ga4gh.vrs

Pull Request - State: open - Opened by korikuzma 6 days ago
Labels: priority:high, build

#596 - build: update cool-seq-tool + gene-normalizer

Pull Request - State: open - Opened by korikuzma 6 days ago
Labels: priority:high, build

#595 - build: pin gene-normalizer version to >=0.7.0

Pull Request - State: closed - Opened by korikuzma 19 days ago
Labels: priority:medium, build

#594 - Add `moleculeType` to `SequenceReference`

Issue - State: open - Opened by korikuzma 29 days ago
Labels: enhancement, priority:low

#593 - Merge staging into main

Pull Request - State: closed - Opened by korikuzma about 1 month ago - 1 comment
Labels: priority:high

#592 - build: update cool-seq-tool version in Pipfile

Pull Request - State: closed - Opened by korikuzma about 1 month ago
Labels: priority:medium, build

#591 - feat!: rename residue mode to coordinate type

Pull Request - State: closed - Opened by korikuzma about 1 month ago
Labels: enhancement, priority:medium

#590 - Rename residue mode to coordinate type

Issue - State: closed - Opened by korikuzma about 1 month ago - 1 comment
Labels: enhancement, priority:medium

#589 - build: pin cool-seq-tool version ~=0.9.1

Pull Request - State: closed - Opened by korikuzma about 1 month ago
Labels: priority:medium, build

#588 - Bump cool-seq-tool version

Issue - State: closed - Opened by korikuzma about 1 month ago - 1 comment
Labels: priority:high, build

#587 - Merge staging into main

Pull Request - State: closed - Opened by korikuzma about 2 months ago - 3 comments
Labels: priority:high

#586 - build!: require python >= 3.11

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: priority:high, build

#585 - docs: update readme with vrs versioning

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: documentation, priority:high

#584 - fix(build): update dependency versions in Pipfile

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: bug, priority:high, build

#583 - chore!: rename optional dependency

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: priority:low, chore

#582 - feat!: update models to vrs 2.0.0 community review ballot

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:high, build

#581 - Update models to VRS 2.0.0 Community Review Ballot

Issue - State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:high, build

#580 - cicd: check if PR to main is coming from staging

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#579 - chore: bring back commits on `main` to `staging`

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#578 - style: update ruff configs

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#577 - chore: use base gitignore

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#576 - feat: return MANE gene(s) in normalize endpoint for genomic queries

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:medium

#575 - build: pin cool-seq-tool~=0.6.0

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build

#574 - Docker Changes

Pull Request - State: open - Opened by rajatkapoordfci 7 months ago - 3 comments
Labels: priority:medium, stale

#573 - docs: update vrs versioning

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:low

#572 - docs: update vrs versioning

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:medium

#571 - fix: update ga4gh.vrs + add back response_model configs for FastAPI

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:medium, build

#570 - feat!: add `sequence` to `SequenceLocation`

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:medium

#569 - cicd: allow missing credentials in aws creds detection

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#568 - chore: remove unused files

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:low, chore

#567 - style: ruff format

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: cleanup, priority:high

#566 - fix: TypeError for params that accept union of enums

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:high

#565 - fix: version imports

Pull Request - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: bug, priority:high

#564 - chore: update ebextensions for downloading latest seqrepo instance

Pull Request - State: closed - Opened by korikuzma 7 months ago - 2 comments
Labels: priority:high, chore

#563 - fix(cicd): add reference to stalebot

Pull Request - State: closed - Opened by korikuzma 7 months ago - 2 comments
Labels: bug, priority:low, ci/cd

#562 - docs: update seqrepo version to 2024-02-20

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:low

#561 - build!: update ga4gh.vrs, cool-seq-tool, + gene-normalizer

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build

#560 - cicd: update precommit dependency in pipfile

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#559 - feat: enable more precise logging configuration

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#558 - cicd: update precommit

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#557 - style: update ruff

Pull Request - State: closed - Opened by jsstevenson 7 months ago - 1 comment
Labels: priority:low

#556 - cicd: update workflows/templates from template repo

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#555 - build: update requirements and build system

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#554 - issue in normalizer behavior for transcript sequence location

Issue - State: closed - Opened by ahwagner 8 months ago - 1 comment

#553 - Docker vn

Pull Request - State: open - Opened by rajatkapoordfci 10 months ago - 6 comments

#552 - Add back `vrs_ref_allele_seq` to response

Issue - State: closed - Opened by korikuzma 11 months ago - 2 comments
Labels: enhancement, priority:high

#551 - return gene context info for genomic queries

Issue - State: open - Opened by katiestahl 11 months ago - 10 comments
Labels: enhancement, priority:low

#550 - build: reorganize build metadata (#549)

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#549 - build: reorganize build metadata

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#548 - docs: readme glow-up

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 1 comment
Labels: priority:low

#547 - chore: update license

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#546 - cicd: require priority label on PRs

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#545 - cicd: require priority label on PRs

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#544 - cicd: test install on 3.12

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#543 - add back missing models to openapi.json

Issue - State: closed - Opened by korikuzma 11 months ago - 2 comments
Labels: priority:high, technical debt

#542 - build!: udpate ga4gh.vrs version

Pull Request - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: priority:high, build

#541 - Update to `ga4gh.vrs[extras]` to `2.0.0a5`

Issue - State: closed - Opened by korikuzma 12 months ago
Labels: priority:high, build

#540 - test: only check vrs ids on certain tests

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:medium, test

#539 - build: pin ga4gh.vrs dependency

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:high, build

#538 - Update SeqRepo collection to `2024-02-20`

Issue - State: closed - Opened by korikuzma 12 months ago - 2 comments
Labels: documentation, enhancement, priority:medium

#537 - cicd: fix elastic beanstalk deployment

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: priority:high, ci/cd

#536 - fix: handle cases where gene_context is not found

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:high

#535 - gnomad_vcf_to_protein handle cases where no gene is found

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:high

#534 - pytest-asyncio DeprecationWarning for event_loop

Issue - State: open - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:low, test

#533 - build: modernize build configs

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 2 comments
Labels: priority:medium, build

#532 - style: replace black with ruff

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: cleanup, priority:medium

#531 - Modernize build configs

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: priority:low, chore

#530 - Remove black and update ruff config

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: cleanup, priority:low, build

#529 - feat!: add more support for queries in gnomad_vcf_to_protein

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 8 comments
Labels: enhancement, priority:medium

#528 - build!: update cool-seq-tool + ga4gh.vrs versions

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 5 comments
Labels: priority:high, build

#527 - Reduce the number of tests

Issue - State: open - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:low, test

#526 - Use biocommons.hgvs for parsing HGVS expressions

Issue - State: open - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:medium, technical debt, build

#525 - fix: hgvs/free text dup/del end positions for definite ranges

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium, vrs-2-alpha

#524 - Fix hgvs/free text dup/del end range positions

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: bug, priority:high, vrs-2-alpha

#523 - feat: expose cool-seq-tool feature overlap endpoint

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high

#522 - Consider lazy loading for class attributes

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:low, technical debt

#521 - Expose cool-seq-tool get_grch38_mane_gene_cds_overlap endpoint

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, priority:high

#520 - fix: vrs-python translator import statement

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high

#519 - Add basic API endpoint tests

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:medium, test

#518 - Update /translate_from

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: bug, priority:high, vrs-2-alpha

#517 - build!: update depdency versions

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, build

#516 - fix: pin versions + fix /translate_identifier

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high, build

#515 - build!: update depdency versions

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 4 comments
Labels: priority:medium, build

#514 - cicd: update release.yml (publish python distribution to pypi)

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd

#513 - cicd: update release.yml (publish python distribution to pypi)

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd

#512 - feat!: update to vrs 2.0-alpha

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high

#511 - fix: catch pydantic ValidationError in parsed to cnv endpoints

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium

#510 - cicd: update elastic beanstalk eb extensions for python3.11 + p7zip

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd

#509 - Update prod AWS instance to python3.11

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:medium, chore

#508 - feat!: add / update to copy number methods from metaschema branch

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high

#507 - fix: still return a result for protein/cdna with no mane data found

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: bug, priority:high

#506 - If genomic query fails getting liftover/mane, try using original input to return a response

Issue - State: open - Opened by korikuzma over 1 year ago - 2 comments
Labels: enhancement, priority:medium

#505 - refactor branch: if no mane data is found, still return a result

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: bug, priority:high

#504 - fix: _get_priority_translation_result using wrong variable

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high

#503 - Refactor

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

#502 - Investigate VRS IDs changing for protein free text queries on refactor branch using /normalize

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: bug, priority:high

#501 - fix: add condition when there are no valid results in /to_vrs

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium

#500 - Add condition when there are no valid results in /to_vrs

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: bug, priority:high

#499 - Stabilize construction of required resources

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment
Labels: priority:low, technical debt

#498 - Add new endpoint for lifting over SPDI + using vrs-python translate from

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

GitHub / cancervariants/variation-normalization issues and pull requests