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.

Sign up for GitHub

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

Jump to bottom

feat: Annotate SVs with somatic SV observation frequencies #1194

Merged
merged 20 commits into from Aug 1, 2023
Merged

feat: Annotate SVs with somatic SV observation frequencies #1194

merged 20 commits into from Aug 1, 2023

Conversation

khurrammaqbool
Copy link
Contributor

@khurrammaqbool khurrammaqbool commented Jul 10, 2023 •
edited

This PR:

Added: The annotation of somatic SVs from somatic SV observations frequencies.

Review and tests:

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

@khurrammaqbool khurrammaqbool requested a review from a team July 10, 2023 10:51
@khurrammaqbool khurrammaqbool self-assigned this Jul 10, 2023
@khurrammaqbool khurrammaqbool linked an issue Jul 10, 2023 that may be closed by this pull request
Annotate clinically relevant SVs with somatic variant observation frequencies from LoqusDB #1193
Closed
@codecov
Copy link

codecov bot commented Jul 10, 2023 •
edited

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (7c71000) 99.36% compared to head (f244d6f) 99.37%.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1194   +/-   ##
========================================
  Coverage    99.36%   99.37%           
========================================
  Files           38       38           
  Lines         1903     1905    +2     
========================================
+ Hits          1891     1893    +2     
  Misses          12       12
Flag Coverage Δ
unittests 99.37% <100.00%> (+<0.01%) ⬆️

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

Files Changed Coverage Δ
BALSAMIC/utils/rule.py 94.61% <100.00%> (+0.08%) ⬆️

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@khurrammaqbool
Copy link
Contributor Author

Screenshot 2023-07-18 at 11 05 39

ivadym
ivadym reviewed Jul 20, 2023
View reviewed changes
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.

Nice, looks good 👍

BALSAMIC/constants/cluster_analysis.json Outdated Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Show resolved Hide resolved
@khurrammaqbool
Copy link
Contributor Author

Nice, looks good 👍

Thank you @ivadym for the review. I have addressed almost all of them and opened issues that fell outside the scope of this PR. Although some of the refactoring could also be taken to another PR, but I made those changes here.

ivadym
ivadym approved these changes Jul 31, 2023
View reviewed changes
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.

Nice 💯

Thanks for addressing my comments @khurrammaqbool 🥇

BALSAMIC/constants/cluster_analysis.json Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vep.rule Show resolved Hide resolved
@sonarcloud
Copy link

sonarcloud bot commented Aug 1, 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 4 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@khurrammaqbool khurrammaqbool merged commit 749c4bb into develop Aug 1, 2023
22 checks passed
@khurrammaqbool khurrammaqbool deleted the feat/add_ldb_somatic_sv_annotation branch August 1, 2023 11:42
@ivadym ivadym mentioned this pull request Nov 6, 2023
Merged
@ivadym ivadym mentioned this pull request Jan 15, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ivadym ivadym ivadym approved these changes

Assignees

@khurrammaqbool khurrammaqbool

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Annotate clinically relevant SVs with somatic variant observation frequencies from LoqusDB
2 participants
@khurrammaqbool @ivadym