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Clinical-Genomics
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chanjo2
Persistent coverage analysis tool using the d4 format
https://clinical-genomics.github.io/chanjo2/
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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
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