clinical-genomics/chanjo2 issues and pull requests

#390 - Update schug to 1.6.2 + other updates

Pull Request - State: open - Opened by northwestwitch 2 months ago - 3 comments

#389 - Update schug library to v.1.6.2

Issue - State: open - Opened by northwestwitch 2 months ago
Labels: dependencies

#388 - Fix the healthcheck step of the docker-compose MySQL file

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 3 comments

#387 - docker-compose example with MySQL database doesn't work any more

Issue - State: closed - Opened by northwestwitch 2 months ago
Labels: Bug

#385 - Minor release 2.1

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 2 comments

#384 - Modified intervals endpoint to return complete info on genes, transcripts and exons

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 3 comments

#383 - Modify genes, transcripts, exons endpoints to return complete info

Issue - State: closed - Opened by northwestwitch 4 months ago - 1 comment
Labels: Enhancement

#382 - Replace custom badges with bootstrap badges

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 3 comments

#381 - From genes overview page (case with WGS), clicking on gene links causes the page to crash

Issue - State: closed - Opened by northwestwitch 4 months ago - 2 comments
Labels: Bug

#380 - Switch to Bootstrap 5 badges

Issue - State: closed - Opened by northwestwitch 4 months ago

#379 - Add refseq transcript names on genes overview page

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 2 comments

#378 - Expand genes overview with refseq XM_ and NM_ accessions

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: Enhancement

#377 - Update libs including schug and starlette

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 3 comments

#376 - Update starlette to address security issue

Issue - State: closed - Opened by northwestwitch 4 months ago - 1 comment
Labels: task

#375 - Support for custom panel probes

Issue - State: closed - Opened by Jakob37 4 months ago - 6 comments

#374 - Add MANE overview report to the documentation

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 2 comments

#373 - Include MANE overview endpoint in the docs

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: Documentation

#372 - Major release 2.0

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 9 comments

#371 - Save Ensembl transcript ID and exon number in exons table

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 4 comments

#370 - Save transcript_id info and exon number in exons database documents

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: Effort S, Enhancement, Gain M

#369 - Add exons stats to gene overview

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 14 comments

#368 - Fom MANE overview, link out to gene overview

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 7 comments

#367 - Link out to gene overview from MANE genes overview

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: Effort S, Enhancement, Gain M

#366 - Add exon coverage to the gene overiew

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: Enhancement

#365 - MANE transcripts report

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 4 comments

#364 - Gene overview crashes when GAREM gene is requested

Issue - State: closed - Opened by northwestwitch 5 months ago - 3 comments
Labels: Bug

#363 - Include all transcripts in report and genes overview.

Issue - State: open - Opened by northwestwitch 5 months ago - 3 comments
Labels: Enhancement, question

#362 - Bump cryptography from 42.0.8 to 43.0.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#361 - Speedup gene overview

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 22 comments

#360 - Fix link for switching between overview thresholds

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 5 comments

#359 - Link directly to overview report on case page

Issue - State: closed - Opened by Jakob37 5 months ago - 2 comments

#358 - Sorted intervals into d4 functions

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 3 comments

#357 - Gene page performance

Issue - State: closed - Opened by Jakob37 5 months ago - 4 comments
Labels: Enhancement, Gain L, Refactor

#356 - Changed coverage links on overview page broken

Issue - State: closed - Opened by Jakob37 5 months ago - 8 comments
Labels: Bug

#354 - MANE transcripts

Issue - State: closed - Opened by Jakob37 5 months ago - 5 comments
Labels: Enhancement

#352 - Separate coverage stats handler

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 2 comments

#351 - Handle the fact that d4tools sorts intervals by chrom, start and stop when calculating coverage

Issue - State: closed - Opened by northwestwitch 5 months ago

#350 - Update d4tools to the latest master branch (both tests and Dockerfile)

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 3 comments

#349 - Replace completeness multitasker with d4tools perc_cov

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 29 comments

#348 - Fixed colors in logging

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 3 comments

#347 - General report with coverage over the entire genome when no genes or gene panels are provided

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#346 - Reintroduce colors in logging

Issue - State: closed - Opened by northwestwitch 6 months ago
Labels: Bug

#345 - d4_genes_condensed_summary to return nan & inf coverage values when error occurs

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#344 - Informative error message from summary when submitted file is wrong

Issue - State: closed - Opened by northwestwitch 6 months ago

#343 - Refactor gene overview and coverage endpoints to obtain completeness from d4tools

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments
Labels: Enhancement, Refactor

#342 - Update pytest to address a ReDoS vulnerability

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments

#341 - Update dependencies including certifi to address dependabot alert

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments

#340 - Refactor report/overview code so coverage completeness is obtained directly from d4tools

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments
Labels: Enhancement, Refactor

#339 - Sort alphabetically incompletely covered genes on report

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#338 - Genes overview endpoint to accept only form data

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#337 - Order incompletely covered genes on report

Issue - State: closed - Opened by northwestwitch 6 months ago
Labels: Enhancement

#336 - Modify overview endpoint to only accept form data

Issue - State: closed - Opened by northwestwitch 6 months ago - 1 comment
Labels: Enhancement, Refactor

#335 - Modified report endpoint to accept only requests with x-www-form-urlencoded form data

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 9 comments

#334 - Replaced deprecated Pydantic parse_obj method with model_validate

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#333 - Fix starlette.templating deprecation warning

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments

#332 - The `parse_obj` method is deprecated

Issue - State: closed - Opened by northwestwitch 6 months ago

#331 - The `name` is not the first parameter anymore. The first parameter should be the `Request` instance.

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

#330 - Do not save cases/samples into the sql database and work uniquely with stats runned on d4 files on the fly

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 7 comments

#329 - Simplify app by not saving cases and samples into the database

Issue - State: closed - Opened by northwestwitch 7 months ago
Labels: Effort M, Refactor

#328 - Check that d4 files provided to condensed stats endpoints are valid

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments

#327 - Expand coverage report explanation to better understand how coverage and coverage completeness values were calculated

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 4 comments

GitHub / clinical-genomics/chanjo2 issues and pull requests