cancervariants/variation-normalization issues and pull requests

#402 - Issue 394 metaschema

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:high

#401 - Document branch / version tracking

Issue - State: closed - Opened by korikuzma almost 2 years ago - 3 comments
Labels: documentation, priority:low, stale

#400 - Add support for HGVS repeated nomenclature

Issue - State: open - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:medium

#400 - Add support for HGVS repeated nomenclature

Issue - State: open - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement, priority:medium

#399 - refactor!: initial cleanup of tokenizers (metaschema-update)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#398 - Use FastAPIRouter

Issue - State: open - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:low, technical debt

#397 - refactor: Allow option to use existing gene-normalizer instance (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#397 - refactor: Allow option to use existing gene-normalizer instance (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#396 - refactor: Allow option to use existing gene-normalizer instance

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#395 - refactor!: initial cleanup of tokenizers

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:medium, technical debt

#394 - Add support for VRS 1.3

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement, priority:high

#394 - Add support for VRS 1.3

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement, priority:high

#393 - feat: add support for amino acids after del (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:low

#393 - feat: add support for amino acids after del (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:low

#392 - refactor!: update cool-seq-tool (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt, build

#391 - refactor!: update cool-seq-tool

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#391 - refactor!: update cool-seq-tool

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, technical debt

#390 - Only use SeqRepoAccess from cool-seq-tool

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:medium, technical debt, build

#390 - Only use SeqRepoAccess from cool-seq-tool

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:medium, technical debt, build

#389 - Validation errors for HGVS variants with refseq IDs when gene DB isn't populated

Issue - State: closed - Opened by jsstevenson almost 2 years ago - 2 comments
Labels: bug, priority:low

#388 - Queryhandler concurrent access fix

Pull Request - State: closed - Opened by theferrit32 almost 2 years ago - 9 comments

#387 - Improve exception handling

Issue - State: open - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:medium, technical debt

#386 - feat: add support for amino acids after del

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:medium

#385 - fix: add support for ambiguous N IUPAC code for cDNA + genomic

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: bug, priority:medium

#384 - fix: add support for ambiguous N IUPAC code for cDNA + genomic (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: bug, priority:medium

#383 - Add support for N ambiguity code

Issue - State: closed - Opened by korikuzma almost 2 years ago - 3 comments
Labels: bug, priority:low

#382 - fix: remove duplicate warnings in gnomad_vcf_to_protein (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: bug, priority:low

#381 - refactor: replace AminoAcidCache with bioutils (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:low, technical debt

#380 - feat: expose cool-seq-tool alignment mapper endpoints

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement, priority:high

#379 - Expose p -> g and c-> g endpoints from cool-seq-tool

Issue - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:high

#379 - Expose p -> g and c-> g endpoints from cool-seq-tool

Issue - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement, priority:high

#378 - Add support for nucleotides after del

Issue - State: closed - Opened by korikuzma almost 2 years ago - 3 comments
Labels: enhancement, priority:medium

#377 - cicd: revert dev termination time back to 12 hours

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, ci/cd

#376 - build: update dependencies (staging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, build

#375 - fix: TypeError in _is_grch38_assembly (stgaging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: bug, priority:medium

#375 - fix: TypeError in _is_grch38_assembly (stgaging)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: bug, priority:medium

#374 - fix: TypeError in _is_grch38_assembly

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: bug, priority:medium

#373 - build: update dependencies

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:medium, build

#372 - Internal server error when querying `/normalize?q=NG_008212.3:g.5426_5445del`

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: bug, priority:medium

#372 - Internal server error when querying `/normalize?q=NG_008212.3:g.5426_5445del`

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: bug, priority:medium

#371 - build(deps): bump starlette from 0.22.0 to 0.25.0

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

#370 - build(deps): bump ipython from 8.9.0 to 8.10.0

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

#369 - Decrease initial startup time

Issue - State: closed - Opened by korikuzma about 2 years ago - 2 comments
Labels: performance, priority:medium, stale

#368 - Allow for option to use existing `QueryHandler` instance from gene-normalizer

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, priority:low

#368 - Allow for option to use existing `QueryHandler` instance from gene-normalizer

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, priority:low

#367 - feat: add support for amplification queries (main)

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

#366 - refactor: replace AminoAcidCache with bioutils

Pull Request - State: closed - Opened by korikuzma about 2 years ago
Labels: priority:low, technical debt

#365 - Replace amino acid cache with bioutils

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: priority:low, technical debt

#365 - Replace amino acid cache with bioutils

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: priority:low, technical debt

#364 - Add lucid diagram to docs

Issue - State: open - Opened by korikuzma about 2 years ago - 2 comments
Labels: documentation, priority:low

#363 - Fix classifications and sequence ontology codes

Issue - State: closed - Opened by korikuzma about 2 years ago - 4 comments
Labels: bug, priority:high

#362 - Add more support for deletions/insertions `gnomad_vcf_to_protein`

Issue - State: closed - Opened by korikuzma about 2 years ago - 8 comments
Labels: enhancement, priority:high, requirement

#361 - Add support for batch queries

Issue - State: open - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, priority:medium

#360 - MVP

Issue - State: closed - Opened by wesleygoar about 2 years ago
Labels: epic

#359 - MVP

Issue - State: closed - Opened by wesleygoar about 2 years ago
Labels: epic

#359 - MVP

Issue - State: closed - Opened by wesleygoar about 2 years ago
Labels: epic

#358 - OSError: [Errno 9] b'Bad file descriptor'

Issue - State: closed - Opened by korikuzma about 2 years ago - 2 comments
Labels: bug, priority:medium

#357 - Add support for HGVS c. queries on intronic site and translate to protein representation

Issue - State: open - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, priority:high

#356 - fix: remove duplicate warnings in gnomad_vcf_to_protein

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

#355 - gnomad_vcf_to_protein returns duplicate warnings

Issue - State: closed - Opened by korikuzma about 2 years ago - 2 comments
Labels: bug, priority:low

#354 - change: version

Pull Request - State: closed - Opened by korikuzma about 2 years ago
Labels: priority:low

#353 - perf: gnomad_vcf_to_protein replace call to uta db with df lookup (staging)

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

#352 - build: update dependency versions

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

#351 - build: unpin ga4gh.vrs + bump gene-normalizer (main)

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

#350 - perf: gnomad_vcf_to_protein replace call to uta db with df lookup (main)

Pull Request - State: closed - Opened by korikuzma about 2 years ago
Labels: performance, priority:medium

#349 - Unpin exact pypi versions

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: priority:low, build

#348 - Improve performance for /gnomad_vcf_to_protein

Issue - State: closed - Opened by korikuzma about 2 years ago - 3 comments
Labels: performance, priority:medium

#345 - build(deps): bump certifi from 2022.9.24 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 2 comments

#342 - Add support for (#_?)_(?_#) ambiguous ranges

Issue - State: open - Opened by korikuzma over 2 years ago - 1 comment
Labels: enhancement, priority:high, requirement

#342 - Add support for (#_?)_(?_#) ambiguous ranges

Issue - State: open - Opened by korikuzma over 2 years ago - 2 comments
Labels: enhancement, priority:high, requirement

#332 - Refactor tokenizers

Issue - State: closed - Opened by korikuzma over 2 years ago - 3 comments
Labels: priority:high, technical debt

#331 - Add support for amplication queries

Issue - State: closed - Opened by korikuzma over 2 years ago - 4 comments
Labels: enhancement

#328 - Add support for nucleotides after dup

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

#327 - Expand support for categorical variation wrt VAI needs

Issue - State: closed - Opened by wesleygoar over 2 years ago - 5 comments
Labels: epic, priority:medium

#326 - Oncogenicity SOP

Issue - State: closed - Opened by wesleygoar over 2 years ago - 1 comment
Labels: epic

#320 - reduce ga4gh vrs id checks in tests

Issue - State: closed - Opened by korikuzma over 2 years ago
Labels: priority:low, test

#318 - Change termination time for dev environment

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: priority:low, chore, ci/cd

#318 - Change termination time for dev environment

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: priority:low, chore, ci/cd

#317 - Create CNV as Canonical Variation

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: enhancement, priority:high

#310 - Investigate gnomad_vcf_to_protein misses

Issue - State: closed - Opened by korikuzma over 2 years ago - 3 comments
Labels: bug, priority:high, stale

#309 - Remove translation work from validators

Issue - State: open - Opened by korikuzma over 2 years ago
Labels: priority:high, technical debt

#309 - Remove translation work from validators

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: priority:high, technical debt

#307 - Add codemeta.json

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: priority:low, chore, stale

#291 - Supporting Telomere-to-Telomere Assembly

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: enhancement, priority:low, stale

#287 - Run analysis on CIViC + MOAlmanac data

Issue - State: closed - Opened by korikuzma almost 3 years ago - 41 comments
Labels: epic, priority:high, requirement, analysis

#284 - gnomad_vcf_to_protein warnings for intron variants

Issue - State: open - Opened by korikuzma almost 3 years ago - 3 comments
Labels: enhancement, priority:low

#283 - Follow Conventional Commit Spec

Issue - State: open - Opened by korikuzma almost 3 years ago - 1 comment
Labels: priority:low, chore, ci/cd

#281 - Insertions that are dups should be classified as duplications

Issue - State: open - Opened by korikuzma almost 3 years ago - 3 comments
Labels: bug, priority:low

#261 - Create separate endpoints for specific queries

Issue - State: closed - Opened by korikuzma almost 3 years ago - 3 comments
Labels: enhancement, priority:medium

#249 - gnomad_vcf_to_protein should try longest compatible remaining if mane not found

Issue - State: open - Opened by korikuzma almost 3 years ago - 1 comment
Labels: enhancement, priority:medium

#248 - Fix bugs with Ensembl support

Issue - State: open - Opened by korikuzma almost 3 years ago - 2 comments
Labels: bug, priority:low

#234 - Add support for complex variation

Issue - State: closed - Opened by korikuzma about 3 years ago - 2 comments
Labels: enhancement, priority:medium, requirement, stale

#231 - Look into using vrs-python for VCF translation

Issue - State: open - Opened by korikuzma about 3 years ago - 1 comment
Labels: priority:high, technical debt

#230 - Need ability to parse repeat HGVS expressions in normalizer

Issue - State: open - Opened by larrybabb about 3 years ago - 2 comments
Labels: enhancement, priority:medium

#218 - Support pgx star allele nomenclatures

Issue - State: open - Opened by jsstevenson about 3 years ago - 2 comments
Labels: enhancement, priority:low, stale-exempt

#215 - Some requests are timing out

Issue - State: open - Opened by korikuzma about 3 years ago - 3 comments
Labels: bug, priority:high

#214 - Unable to normalize cancer hotspots terms

Issue - State: open - Opened by korikuzma about 3 years ago - 1 comment
Labels: bug, priority:low

#209 - Add HGVS description to variation descriptor

Issue - State: open - Opened by korikuzma about 3 years ago - 1 comment
Labels: enhancement, priority:low

#208 - Add support for HGVS silent mutations where reference nucleotide is given

Issue - State: open - Opened by korikuzma about 3 years ago - 1 comment
Labels: enhancement, priority:low, requirement

#207 - Update FastAPI schema examples

Issue - State: open - Opened by korikuzma about 3 years ago - 3 comments
Labels: documentation, priority:high, requirement

GitHub / cancervariants/variation-normalization issues and pull requests