Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / GenomicMedLab/cool-seq-tool issues and pull requests

#371 - Add parameter for using GRCh37 sequences

Issue - State: open - Opened by jarbesfeld 10 days ago
Labels: enhancement, priority:medium

#370 - fix: make gene optional param for converting genomic coords as long a…

Pull Request - State: closed - Opened by katiestahl 10 days ago
Labels: bug, priority:high

#369 - Do not require gene when genomic accession and transcript are provided to genomic_to_tx_segment

Pull Request - State: closed - Opened by jarbesfeld 10 days ago
Labels: priority:high

#367 - MANE transcript data was not found for the gene C1orf159

Issue - State: open - Opened by jarbesfeld 23 days ago - 4 comments
Labels: bug, priority:medium

#366 - Ensure that start position does not exceed end position for a transcript segment

Issue - State: open - Opened by jarbesfeld about 1 month ago
Labels: bug, priority:medium

#365 - refactor: remove duplicate `genomic_ac` check

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

#364 - test: update tests for `ExonGenomicCoordsMapper`

Pull Request - State: closed - Opened by korikuzma about 1 month ago - 6 comments
Labels: priority:low, test, stale, keep-alive

#363 - Migrate staging changes to main branch

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

#362 - Break up `_genomic_to_tx_segment` into smaller methods

Issue - State: open - Opened by korikuzma about 2 months ago
Labels: priority:low, technical debt

#361 - Choosing the Correct Adjacent Exon along Exon Boundaries

Issue - State: open - Opened by jarbesfeld about 2 months ago - 3 comments
Labels: bug, priority:medium

#360 - refactor: rename `_get_alt_ac_start_and_end` + flatten output

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

#359 - refactor: rename `is_start` kwarg in private methods to `is_seg_start`

Pull Request - State: closed - Opened by korikuzma about 2 months ago - 1 comment
Labels: priority:low, technical debt

#358 - refactor: reorder classes and methods in `exon_genomic_coords` module

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

#357 - refactor!: rename `ExonCoord` to `_ExonCoord` to indicate internal use

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

#356 - fix: genomic accession mismatch when getting nearest tx junction

Pull Request - State: closed - Opened by korikuzma about 2 months ago - 1 comment
Labels: bug, priority:high

#355 - docs: link to stable, not latest

Pull Request - State: closed - Opened by jsstevenson about 2 months ago
Labels: priority:low

#354 - Update fixtures and offsets for test_exon_genomic_coords

Pull Request - State: closed - Opened by jarbesfeld about 2 months ago
Labels: priority:high

#353 - feat: enable direct import of CST from package root

Pull Request - State: closed - Opened by jsstevenson about 2 months ago
Labels: priority:low

#352 - feat!: update `ExonGenomicCoordsMapper` + `UtaDatabase`

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

#351 - feat!: return Pydantic model in `UtaDatabase.get_tx_exon_aln_v_data`

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

#350 - feat!: return Pydantic model in `get_alt_ac_start_or_end`

Pull Request - State: closed - Opened by korikuzma 2 months ago - 1 comment
Labels: enhancement, priority:medium

#349 - refactor: remove unnecessary literal from `AnnotationLayer` enum

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

#348 - feat!: remove `UtaDatabase.get_tx_exons_genomic_coords`

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

#347 - feat!: remove `UtaDatabase.get_tx_exons` + cleanup exon work

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

#346 - [OLD] feat!: update `ExonGenomicCoordsMapper`

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

#345 - Wrong location in `ExonGenomicCoordsMapper.transcript_to_genomic_coordinates`

Issue - State: closed - Opened by jsstevenson 2 months ago - 3 comments
Labels: bug

#344 - feat!: remove optional `coordinate_type` from `genomic_to_tx_segment`

Pull Request - State: closed - Opened by korikuzma 2 months ago - 2 comments
Labels: priority:medium

#343 - feat!: rename `start`/`end` to `genomic_start`/`genomic_end` in `genomic_to_tx_segment`

Pull Request - State: closed - Opened by korikuzma 2 months ago - 1 comment
Labels: enhancement, priority:medium

#342 - Add information about Ensembl transcripts to docs

Issue - State: open - Opened by korikuzma 2 months ago
Labels: documentation, priority:low

#341 - Add coordinate type to usage docs

Issue - State: open - Opened by korikuzma 2 months ago
Labels: documentation, priority:low

#340 - refactor: remove optional `strand` field from `genomic_to_tx_segment`

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

#339 - feat!: move `get_tx_exons_genomic_coords` to `ExonGenomicCoordsMapper`

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

#338 - feat!: rename ExonGenomicCoordsMapper methods

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

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

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

#336 - Move pydantic models to their respective module

Issue - State: open - Opened by korikuzma 2 months ago
Labels: priority:low, technical debt

#335 - Rename residue mode to coordinate type

Issue - State: closed - Opened by korikuzma 2 months ago - 3 comments
Labels: enhancement

#334 - feat!: Return Pydantic models instead of dicts in UtaDatabase

Pull Request - State: closed - Opened by korikuzma 2 months ago
Labels: priority:medium

#333 - docs: remove VRS schema support section

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

#332 - Counterintuitive/wrong? offset from genomic to transcript mapping

Issue - State: closed - Opened by jsstevenson 2 months ago - 3 comments
Labels: bug, priority:high

#331 - docs: fix source link

Pull Request - State: closed - Opened by jsstevenson 2 months ago
Labels: priority:low

#330 - Add start/end residue mode parameter

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

#329 - "Start chr does not match end chr" when calling `genomic_to_exon_coords` with one position in intronic space

Issue - State: closed - Opened by jsstevenson 2 months ago - 6 comments
Labels: bug, priority:high

#328 - fix(test): remove fixture decorator from get_prioritized_transcripts_from_gene

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

#327 - `GenomicData` should include start/end for both start_exon and end_exon

Issue - State: closed - Opened by korikuzma 2 months ago - 24 comments
Labels: enhancement, priority:medium

#326 - feat: make methods in `ManeTranscript` public

Pull Request - State: closed - Opened by korikuzma 2 months ago - 4 comments
Labels: enhancement, priority:low

#325 - feat: add option to `g_to_grch38` to return a list of MANE gene(s)

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

#324 - fix: correct strand typo

Pull Request - State: closed - Opened by jsstevenson 2 months ago
Labels: priority:high

#323 - Add option to `g_to_grch38` to return a list of MANE gene(s)

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

#322 - feat!: only return cdna representation in `g_to_mane_c`

Pull Request - State: closed - Opened by korikuzma 2 months ago - 1 comment
Labels: enhancement, priority:medium

#321 - chore: remove unused schemas

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

#320 - `g_to_mane_c` should not return genomic representation

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

#319 - cicd: allow missing credentials

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

#318 - cicd: use GML reusable-stale action

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, ci/cd

#317 - chore: rename optional dependency

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, chore

#316 - cicd: update precommit

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

#315 - cicd: update actions and stale settings from template

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

#314 - feat: validate all inputs at once

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

#313 - Validate gene/transcript input requirement in genomic_to_transcript_exon_coordinates

Issue - State: closed - Opened by jsstevenson 3 months ago
Labels: enhancement, priority:low

#312 - fix: handle input of alt_ac, not just chromosome

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

#310 - refactor!: move liftover to separate module

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, technical debt

#309 - fix: resolve DataOrientationWarning for pl.DataFrame

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: bug, priority:low

#308 - fix: update handling ClientErrors when getting aws secret value

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: bug, priority:low

#307 - `SeqRepoAccess` should support `SeqRepoRESTDataProxy`

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

#306 - refactor: use Assembly enum instead of hard coding

Pull Request - State: closed - Opened by korikuzma 3 months ago - 2 comments
Labels: priority:low, technical debt

#305 - feat: consistently handle bare and prefixed chromosome numbering

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

#304 - chore!: remove FastAPI

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, chore

#303 - fix: use correct logging setup

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

#302 - style: update ruff configs

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

#301 - feat!: use setuptools-scm, capture version at package root

Pull Request - State: closed - Opened by jsstevenson 3 months ago - 5 comments
Labels: priority:low

#300 - chore: add stalebot

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

#299 - cicd: use builtin token

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

#298 - chore: add issue templates

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

#297 - feat: enable suppression of latest resource check

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: enhancement, priority:medium

#296 - fix(docs): correct kwarg in docstring example

Pull Request - State: closed - Opened by korikuzma 4 months ago
Labels: bug, priority:low

#295 - build: require >= python 3.10

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:medium

#294 - build: pin polars 1.0

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:low, build

#293 - Double check Polars 1.0 compatibility

Issue - State: closed - Opened by jsstevenson 4 months ago
Labels: build

#292 - feat!: change default postgresql port to 5432

Pull Request - State: closed - Opened by korikuzma 4 months ago
Labels: enhancement, priority:low

#291 - fix: don't use deprecated columns param

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:low, technical debt

#290 - feat!: acquire data with wags-tails, overhaul static file handling

Pull Request - State: closed - Opened by jsstevenson 4 months ago - 2 comments
Labels: priority:low

#289 - Resolve Polars `columns` deprecation warning

Issue - State: closed - Opened by jsstevenson 4 months ago - 1 comment
Labels: priority:medium, technical debt

#288 - Serve on port 5432 by default

Issue - State: closed - Opened by jsstevenson 4 months ago
Labels: bug, priority:medium

#287 - Make default UTA DB URL value programmatically accessible

Issue - State: closed - Opened by jsstevenson 4 months ago
Labels: enhancement, priority:low

#286 - Provide resource availability check methods

Issue - State: closed - Opened by jsstevenson 4 months ago - 1 comment
Labels: enhancement, priority:low

#285 - Consider alternatives to custom `genomic` table

Issue - State: open - Opened by korikuzma 5 months ago - 1 comment
Labels: priority:low, technical debt

#284 - Don't download resource files on import

Issue - State: closed - Opened by jsstevenson 5 months ago - 3 comments
Labels: enhancement, priority:medium

#283 - Clean up UTA setup instructions

Issue - State: closed - Opened by jsstevenson 6 months ago - 2 comments
Labels: documentation, priority:medium, stale

#282 - Allow initialization of writeable SeqRepo instance

Issue - State: open - Opened by jsstevenson 6 months ago - 2 comments
Labels: enhancement, priority:low

#281 - docs: fix residue mode illustration rendering

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

#280 - docs: add badges to main readme

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

#279 - cicd: add priority label check

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

#278 - build: update build metadata

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

#277 - cicd: test in python 3.12

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

#276 - chore: update license

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

#275 - docs: add badges

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

#274 - fix: scope of resp if breakpoint does not occur on an exon

Pull Request - State: closed - Opened by jarbesfeld 7 months ago - 2 comments
Labels: priority:medium

#273 - Fix resp scope for get_nearest_transcript_junction

Issue - State: closed - Opened by jarbesfeld 7 months ago

#272 - build: pin ruff to v0.2.0

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