ga4gh/vrs-python issues and pull requests

#156 - Refactor logging

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: Stale-exempt

#155 - feat: include VRS location digest if identify is True

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

#154 - Include location ID in translate_from responses

Issue - State: closed - Opened by jsstevenson about 2 years ago - 2 comments
Labels: Stale

#153 - Consider resolving pylint `too-many` warnings

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

#152 - refactor: add **kwargs to translate_from signature

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 1 comment

#151 - Validate input + reference sequence in `translate_from`

Issue - State: open - Opened by korikuzma about 2 years ago - 2 comments
Labels: bug, Stale-exempt, priority:high

#150 - Update `translate_from` signature + handling different from_translators

Issue - State: closed - Opened by korikuzma about 2 years ago
Labels: enhancement

#149 - cleanup: resolve pylint warnings

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 4 comments

#148 - feat: Add validation to _from_gnomad in translator

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 2 comments

#147 - Add input validation for _from_gnomad

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

#146 - Add more log statements to VCF Annotator

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

#145 - Add additional log statements to VCF Annotator

Issue - State: closed - Opened by korikuzma about 2 years ago
Labels: enhancement

#144 - Dev installation instructions need clarification

Issue - State: closed - Opened by ahwagner about 2 years ago - 4 comments
Labels: good first issue, documentation, Stale-exempt

#143 - Document the docker tool

Issue - State: open - Opened by ahwagner about 2 years ago - 6 comments
Labels: good first issue, docs, Stale-exempt

#142 - docs: update readme

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

#141 - docs: update README for metaschema-update branch / releases

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 3 comments

#140 - Fix versioning

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment

#139 - feat: add pre-commit hook for pylint

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

#138 - Add pre-commit hook for pylint errors

Issue - State: closed - Opened by korikuzma about 2 years ago

#137 - VCF Annotator handles invalid input + remove VCF ID from key in pickle file for vcf annotation

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

#136 - change: remove VCF ID from key in pickle file for vcf annotation

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

#135 - Remove `record.id` from key in pickle for vcf annotator

Issue - State: closed - Opened by korikuzma about 2 years ago

#134 - feat: VCF Annotator handles invalid input (#132)

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

#133 - Add support for protein variation in translate_to()

Issue - State: open - Opened by jarbesfeld about 2 years ago - 3 comments
Labels: enhancement, Stale-exempt

#132 - VCF Annotator should handle edge cases

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment

#131 - feat: vcf annotator optionally allows output vcf/pickle

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

#130 - Make output paths optional in VCF Annotator

Issue - State: closed - Opened by korikuzma about 2 years ago
Labels: enhancement

#129 - fix: VCF Annotation tests use REST dp

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

#128 - Create online notebook welcome text

Issue - State: closed - Opened by ahwagner about 2 years ago - 3 comments
Labels: good first issue, Stale-exempt

#127 - feat: dockerize vrs-python

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 13 comments

#126 - feat: vcf annotation to allow assembly param (#125)

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 2 comments

#125 - VRS / VCF Annotation Tool should allow for input assembly

Issue - State: closed - Opened by korikuzma about 2 years ago

#124 - Add compression to output pkl file in the VCF-Annotation script

Issue - State: open - Opened by wesleygoar about 2 years ago - 1 comment
Labels: enhancement, Stale-exempt

#123 - feat: VCFAnnotator accepts both seqrepo dps + clean up

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

#122 - VCF / VRS Annotation should allow either local or rest seqrepo dp

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

#121 - VRS / VCF Annotation Tool should allow files from google cloud bucket

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

#120 - PGx tutorial notebooks

Pull Request - State: closed - Opened by ahwagner about 2 years ago - 12 comments

#119 - Containerize + provide endpoint for VCF / VRS annotation

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: Stale

#118 - feat: digests take ordered property in arrays into consideration (#116)

Pull Request - State: closed - Opened by korikuzma over 2 years ago - 1 comment

#117 - Update Genotype & PGx notebook

Issue - State: open - Opened by ahwagner over 2 years ago - 1 comment
Labels: Stale-exempt

#116 - Update `ga4gh_identify` to take the `ordered` property into consideration

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: 2.0-alpha, priority:high, requirement

#115 - Greatly Expanded Readme/Documentation

Issue - State: open - Opened by wesleygoar over 2 years ago - 3 comments
Labels: docs, Stale-exempt

#114 - #113: update VRS-Python with VRS Genotype model

Pull Request - State: closed - Opened by ahwagner over 2 years ago - 3 comments

#113 - Update VRS submodules to get Genotype models

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

#112 - fix: update spdi regex + update tests

Pull Request - State: closed - Opened by korikuzma over 2 years ago - 1 comment

#111 - Unable to translate from SPDI deletions

Issue - State: closed - Opened by korikuzma over 2 years ago
Labels: bug

#110 - Add instructions to Terra notebook

Pull Request - State: closed - Opened by vdauwera over 2 years ago - 6 comments

#109 - Use GitHub releases interface for releases

Issue - State: closed - Opened by jsstevenson over 2 years ago - 6 comments
Labels: Stale-exempt

#108 - add notebook required for terra workspace

Pull Request - State: closed - Opened by korikuzma over 2 years ago - 2 comments

#107 - Add Terra welcome notebook

Issue - State: closed - Opened by korikuzma over 2 years ago

#106 - refactor: Metaschema update

Pull Request - State: closed - Opened by korikuzma over 2 years ago - 2 comments

#105 - Metaschema updates

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: Stale-exempt

#104 - Genotype Model Support for VCF Annotation Script

Issue - State: open - Opened by wesleygoar over 2 years ago - 1 comment
Labels: enhancement, Stale-exempt

#103 - Consider returning Text object in Translator methods instead of None

Issue - State: closed - Opened by korikuzma over 2 years ago - 6 comments
Labels: question, Stale-exempt

#102 - 61 oserror unable to open seqrepo directory usrlocalshareseqrepolatest when using seqrepo

Pull Request - State: closed - Opened by reece over 2 years ago - 2 comments

#100 - Consider adding README for common issues

Issue - State: open - Opened by korikuzma over 2 years ago - 2 comments
Labels: documentation, Stale-exempt

#99 - Issue 93 binder

Pull Request - State: closed - Opened by wesleygoar over 2 years ago

#98 - Add consistent docstrings and type-hints

Issue - State: open - Opened by korikuzma almost 3 years ago - 3 comments
Labels: Stale-exempt

#97 - Resolve pylint errors

Issue - State: closed - Opened by korikuzma almost 3 years ago - 3 comments
Labels: Stale-exempt

#95 - Extend translator methods

Issue - State: open - Opened by korikuzma almost 3 years ago - 2 comments
Labels: enhancement, Stale-exempt

#93 - Jupyter Notebooks in the Cloud

Issue - State: closed - Opened by korikuzma almost 3 years ago - 4 comments
Labels: enhancement

#85 - retrieve schema version

Issue - State: open - Opened by ahwagner almost 3 years ago - 3 comments
Labels: Stale-exempt

#78 - Issue 77: Fix TypeError in _to_spdi

Pull Request - State: closed - Opened by korikuzma almost 3 years ago - 1 comment

#75 - Core module and VRSATILE

Issue - State: open - Opened by ahwagner almost 3 years ago - 8 comments
Labels: Stale-exempt

#67 - add MANIFEST.in

Pull Request - State: closed - Opened by ahwagner about 3 years ago - 1 comment

#65 - VCF Support

Issue - State: closed - Opened by ahwagner about 3 years ago - 8 comments
Labels: Stale-exempt

#61 - OSError: Unable to open SeqRepo directory /usr/local/share/seqrepo/latest when using seqrepo

Issue - State: closed - Opened by algarsi3 over 3 years ago - 6 comments
Labels: Stale-exempt

#60 - Revert "Fix bug in _from_hgvs when using SeqRepoDataProxy"

Pull Request - State: closed - Opened by reece over 3 years ago

GitHub / ga4gh/vrs-python issues and pull requests