Fix #4906 - warn on potentially conflicting ACMG terms. #4932
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #4932 +/- ##
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+ Coverage 84.80% 84.81% +0.01%
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Files 320 320
Lines 19335 19344 +9
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+ Hits 16397 16407 +10
+ Misses 2938 2937 -1 ☔ View full report in Codecov by Sentry. |
dnil
commented
Oct 10, 2024
scout/constants/acmg.py
Outdated
| @@ -297,7 +297,7 @@ | |||
| ( | |||
| "BP7", | |||
| { | |||
| "short": "(not in use)", | |||
| "short": "Synonymous, no splice impact", | |||
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I’m going to guess that was from before we had splice prediction in the pipe.
northwestwitch
approved these changes
Oct 11, 2024
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
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dnil
added a commit
that referenced
this pull request
Oct 11, 2024
* Fix #4906 - warn on potentially conflicting ACMG terms. * add a tuple, sort, and simplify slightly * add test * typo * Update scout/constants/acmg.py Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com> * Update scout/utils/acmg.py Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com> --------- Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
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This PR adds a functionality or fixes a bug.
Thanks to @4WGH for highlighting this and for a good discussion on potential pairs.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: