Clinical-Genomics chanjo2 issues

Clinical-Genomics / chanjo2

Persistent coverage analysis tool using the d4 format

https://clinical-genomics.github.io/chanjo2/

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issues

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

#347 northwestwitch opened 1 week ago
2
Reintroduce colors in logging

#346 northwestwitch opened 1 week ago
0
d4_genes_condensed_summary to return nan & inf coverage values when error occurs

#345 northwestwitch closed 2 weeks ago
3
Informative error message from summary when submitted file is wrong

#344 northwestwitch closed 2 weeks ago
0
Refactor gene overview and coverage endpoints to obtain completeness from d4tools

#343 northwestwitch opened 3 weeks ago
2
Update pytest to address a ReDoS vulnerability

#342 northwestwitch closed 3 weeks ago
2
Update dependencies including certifi to address dependabot alert

#341 northwestwitch closed 3 weeks ago
2
Refactor report/overview code so coverage completeness is obtained directly from d4tools

#340 northwestwitch opened 3 weeks ago
2
Sort alphabetically incompletely covered genes on report

#339 northwestwitch closed 1 month ago
3
Genes overview endpoint to accept only form data

#338 northwestwitch closed 1 month ago
3
Order incompletely covered genes on report

#337 northwestwitch closed 1 month ago
0
Modify overview endpoint to only accept form data

#336 northwestwitch closed 1 month ago
1
Modified report endpoint to accept only requests with x-www-form-urlencoded form data

#335 northwestwitch closed 1 month ago
9
Replaced deprecated Pydantic parse_obj method with model_validate

#334 northwestwitch closed 1 month ago
3
Fix starlette.templating deprecation warning

#333 northwestwitch closed 1 month ago
3
The `parse_obj` method is deprecated

#332 northwestwitch closed 1 month ago
0
The `name` is not the first parameter anymore. The first parameter should be the `Request` instance.

#331 northwestwitch closed 1 month ago
0
Do not save cases/samples into the sql database and work uniquely with stats runned on d4 files on the fly

#330 northwestwitch closed 3 weeks ago
7
Simplify app by not saving cases and samples into the database

#329 northwestwitch closed 3 weeks ago
0
Check that d4 files provided to condensed stats endpoints are valid

#328 northwestwitch closed 1 month ago
3
Expand coverage report explanation to better understand how coverage and coverage completeness values were calculated

#327 northwestwitch closed 1 month ago
4
Handle errors for condensed stats endpoint

#326 northwestwitch closed 1 month ago
0
Clarify "Average coverage"

#325 Jakob37 closed 1 month ago
2
Update pyproject.toml

#324 northwestwitch closed 2 months ago
1
Minor release 1.9

#323 northwestwitch closed 2 months ago
1
Docs for the new coverage condensed summary endpoint

#322 northwestwitch closed 2 months ago
1
Condensed stats for different samples over a list of genes

#321 northwestwitch closed 2 months ago
3
Avoid uvicorn logger and use __main__ logger and remove logger from multiprocessing code

#320 northwestwitch closed 2 months ago
6
Minimal stats endpoint for delivery reports in scout

#319 northwestwitch closed 2 months ago
3
Fix tests GitHub action to use d4tools 0.3.10

#318 northwestwitch closed 2 months ago
1
Update Dockefile to use d4tools 0.3.10

#317 northwestwitch closed 2 months ago
5
Improve performance of get_coverage_completeness.py

#316 Jakob37 opened 2 months ago
7
Update dependencies to address security alerts

#315 northwestwitch closed 2 months ago
3
Address security alerts

#314 northwestwitch closed 2 months ago
0
Minor release 1.8

#313 northwestwitch closed 2 months ago
2
Added cryptography dependency

#312 northwestwitch closed 3 months ago
3
Simplify and generalise issue templates

#311 northwestwitch closed 3 months ago
1
Simpler Pull Request template

#310 northwestwitch closed 3 months ago
1
Move logging setup outside lifespan and db initialisation logic

#309 northwestwitch closed 3 months ago
3
Startup errors crashing in log statement

#308 Jakob37 closed 1 month ago
19
Updated version of external images used in GitHub actions

#307 northwestwitch closed 3 months ago
2
Warnings by the black (lint) action

#306 northwestwitch closed 3 months ago
0
Prepare release 1.7

#305 northwestwitch closed 3 months ago
5
Remove pyd4 from chanjo Docker image

#304 northwestwitch closed 3 months ago
5
Fix cov stats by running b4tools stat for each line of a bed file

#303 northwestwitch closed 3 months ago
7
Temp fix the d4tools super high region coverage bug #78

#302 northwestwitch closed 3 months ago
40
Create an environment.yml file to quickly initialize the environment when reinstalling the repo

#301 northwestwitch closed 3 months ago
3
Can't install mysqlclient on macOS

#300 northwestwitch closed 3 months ago
0
Occasionally large differences in coverage for same gene region in same sample

#299 Jakob37 closed 2 months ago
11
Fix 'show genes' checkbox position on report

#298 northwestwitch closed 4 months ago
3