Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: Add annotation for somatic observation frequencies from loqusDB #1187

Merged
merged 4 commits into from Jun 27, 2023

Conversation

khurrammaqbool
Copy link
Contributor

This PR:

Added: Annotation for somatic observation frequencies from loqusDB.

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@codecov
Copy link

codecov bot commented Jun 26, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (cbf4577) 99.28% compared to head (dd544ec) 99.28%.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #1187   +/-   ##
========================================
  Coverage    99.28%   99.28%           
========================================
  Files           29       29           
  Lines         1682     1684    +2     
========================================
+ Hits          1670     1672    +2     
  Misses          12       12           
Flag Coverage Δ
unittests 99.28% <100.00%> (+<0.01%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
BALSAMIC/utils/rule.py 95.03% <100.00%> (+0.07%) ⬆️

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

@khurrammaqbool
Copy link
Contributor Author

Screenshot 2023-06-26 at 16 05 42

Copy link
Contributor

@ivadym ivadym left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good 👍

BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
tests/conftest.py Show resolved Hide resolved
BALSAMIC/workflows/balsamic.smk Outdated Show resolved Hide resolved
@ivadym
Copy link
Contributor

ivadym commented Jun 27, 2023

Btw, have you seen my comment here: #1178 (comment)?

We should be careful when renaming CLIs that are being used in CG in order to keep up to date with the changes

@sonarcloud
Copy link

sonarcloud bot commented Jun 27, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@khurrammaqbool khurrammaqbool merged commit 82f3915 into develop Jun 27, 2023
22 checks passed
@khurrammaqbool khurrammaqbool deleted the feat/add_ldb_somatic_snv_annotation branch June 27, 2023 11:56
@ivadym ivadym mentioned this pull request Nov 6, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Annotate clinically relevant SNVs with somatic variant observation frequencies from LoqusDB
2 participants