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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

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khurrammaqbool
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@khurrammaqbool khurrammaqbool commented Jul 10, 2023 •
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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
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codecov bot commented Jul 10, 2023 •
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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%) ⬆️

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@khurrammaqbool
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Screenshot 2023-07-18 at 11 05 39

ivadym
ivadym reviewed Jul 20, 2023
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Nice, looks good 👍

BALSAMIC/constants/cluster_analysis.json Outdated Show resolved Hide resolved
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@khurrammaqbool
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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
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Nice 💯

Thanks for addressing my comments @khurrammaqbool 🥇

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sonarqubecloud 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
@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
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@ivadym ivadym mentioned this pull request Jan 15, 2024
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@ivadym ivadym ivadym approved these changes

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