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
#368 - Gene should be an optional parameter for genomic_to_tx_segment when transcript and genomic accession are provided
Issue -
State: closed - Opened by jarbesfeld 15 days ago
Labels: bug, priority:medium
#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
#311 - `AttributeError` from only supplying `alt_ac` for getting nearest tx junction in `genomic_to_transcript_exon`
Issue -
State: closed - Opened by jsstevenson 3 months ago
Labels: bug
#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