cancervariants/variation-normalization issues and pull requests

#497 - Add support for SPDI nomenclature in /to_vrs and /normalize

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

#496 - refactor: rm lingering structural_type

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

#495 - Fix GH Action installing deps

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: priority:low, ci/cd, stale

#494 - refactor!: clean up app (metaschema)

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

#493 - Considering adding vulture pre-commit hook

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

#492 - Update metaschema to pull in refactor changes

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

#491 - fix: add `input_assembly` param for gnomad vcf / genomic free text queries

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

#490 - Adding input assembly for gnomad vcf queries

Issue - State: open - Opened by korikuzma over 1 year ago - 2 comments
Labels: bug, vrs-2-alpha

#489 - refactor: gnomad vcf is classified as delins/sub/ref agree

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

#488 - refactor: remove duplicated validation code in genomic deletion

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

#487 - refactor!: remove structural type from variation descriptor

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

#486 - Remove structural type from variation descriptor response

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments

#485 - refactor: use cool-seq-tool AnnotationLayer and rm CoordinateType

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

#484 - fix: hgvs dup del mode dels should be allele w lse

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

#483 - chore: have black run before ruff + have it autofix

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

#482 - fix: default mode for hgvs dup del mode wrt rse

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

#481 - Parameterize `vrs_ref_allele_seq`

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

#480 - refactor: remove pyliftover from deps + remove unnecessary check

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

#479 - feat: add more support for gnomad VCF expressions in normalize

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

#478 - Add more support for gnomad VCF expressions

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

#477 - Improve free text query performance

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

#476 - Update metaschema to use VRS 2.0-alpha changes

Issue - State: closed - Opened by korikuzma over 1 year ago - 6 comments
Labels: enhancement, priority:high

#475 - Replace flake8 with ruff

Issue - State: closed - Opened by jsstevenson over 1 year ago - 6 comments
Labels: cleanup, priority:medium

#474 - refactor!: clean up app

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 5 comments
Labels: priority:high, technical debt

#473 - No gene symbol found for `ENST00000277541.6`

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

#472 - cicd: update sc_product_id

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

#471 - Add more tests for HGVS Ensembl expressions

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

#470 - Update codebuild sc product id

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:medium, ci/cd

#469 - fix: allow comparator to be set in start/end values

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

#468 - fix: Copy Number Count copies should be Number or Indef/Def Range

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

#467 - Better error and warning handling

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

#466 - Add FAQ Docs

Issue - State: open - Opened by korikuzma over 1 year ago
Labels: documentation

#465 - Parsed to CNV endpoints do not cover all ambiguous ranges

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

#464 - Add support for NG expressions

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

#463 - Support NCBI36 / hg18

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

#462 - build: update ga4gh.vrsatile.pydantic version

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

#461 - build: update ga4gh.vrsatile.pydantic version

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

#460 - refactor!: parsed to copy number should accept request body (metaschema)

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

#459 - feat: add do_liftover param in parsed to copy number endpoints (metaschema)

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

#458 - parsed to copy number should accept request body rather than query params

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

#457 - hgvs_to_copy_number_count should support 0 baseline_copies

Issue - State: open - Opened by theferrit32 over 1 year ago - 1 comment

#456 - chore: update elastic beanstalk commands

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

#455 - fix!: `/parsed_to_cn_var` should accept number, definite range, and indefinite range

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

#454 - Remove /to_canonical_variation endpoint

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments

#453 - feat: add parsed to copy number change endpoint (metaschema)

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

#452 - ci: add GH action for installing deps + remove requirements (metaschema)

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

#451 - parsed to copy number endpoints should allow curie or gene as subject

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

#450 - parsed to copy number endpoints should have a do_liftover param

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

#449 - to_vrs returns valid results when hgvs position is greater than ref sequence length

Issue - State: open - Opened by larrybabb over 1 year ago - 2 comments
Labels: bug

#448 - Update FastAPI descriptions

Issue - State: open - Opened by korikuzma over 1 year ago
Labels: documentation

#447 - gnomad_vcf_to_protein gives incorrect VRS variation

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

#446 - revert: analysis: civic + moa variant analysis (#439)

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

#445 - Remove analysis notebooks

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

#444 - Create parsed_to_cx_var endpoint

Issue - State: closed - Opened by korikuzma over 1 year ago - 3 comments
Labels: enhancement, priority:high

#443 - /parsed_to_cn_var should accept number, indefinite range, or definite range

Issue - State: open - Opened by korikuzma over 1 year ago - 3 comments
Labels: bug, priority:low

#442 - ci: add GH action for installing deps + remove requirements

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

#441 - Add flake8-nb for analysis work

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

#440 - refactor: cleanup civic + moa evidence/assertion analysis notebook

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

#439 - analysis: civic + moa variant analysis

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 6 comments
Labels: priority:medium, analysis

#438 - server error on /to_vrs and /normalize for "NC_000010.11-87925523-C-G"

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment

#437 - build(deps-dev): bump tornado from 6.3.1 to 6.3.2

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

#436 - Add more tests for incorrect input

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

#435 - build(deps): bump requests from 2.30.0 to 2.31.0

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

#434 - Add support for HGVS insertions of form {pos}_{pos}ins{pos}_{pos}

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

#433 - build(deps): bump starlette from 0.26.1 to 0.27.0

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

#432 - GENIE Analysis

Issue - State: closed - Opened by korikuzma almost 2 years ago - 10 comments
Labels: priority:high, analysis

#431 - GENIE Analysis

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

#430 - refactor: create / update / remove enums in schemas

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

#429 - Some fields can be inherited from another class (but this requires renaming of fields to a more generalized name rather than specific to the class itself)

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

#428 - Some fields like `so_id` and `molecule_context` are in Tokenizer schemas, but should be moved to Classification schemas. For `molecule_context` we should use ga4gh.vrsatile.pydantic

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

GitHub / cancervariants/variation-normalization issues and pull requests