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feat(finemapping): susie method #398

Merged
merged 35 commits into from
Feb 8, 2024
Merged

feat(finemapping): susie method #398

merged 35 commits into from
Feb 8, 2024

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Daniel-Considine
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Adding SUSIE Class and methods for fine-mapping.

Daniel-Considine and others added 4 commits January 9, 2024 10:38
Bumps [ipykernel](https://github.com/ipython/ipykernel) from 6.27.1 to 6.28.0.
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md)
- [Commits](ipython/ipykernel@v6.27.1...v6.28.0)

---
updated-dependencies:
- dependency-name: ipykernel
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@Daniel-Considine Daniel-Considine marked this pull request as ready for review January 9, 2024 12:21
@Daniel-Considine Daniel-Considine marked this pull request as draft January 9, 2024 12:22
@Daniel-Considine Daniel-Considine marked this pull request as ready for review January 11, 2024 14:19
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codecov-commenter commented Jan 11, 2024

Codecov Report

Attention: 163 lines in your changes are missing coverage. Please review.

Comparison is base (42b366c) 85.67% compared to head (2c6619f) 86.10%.
Report is 108 commits behind head on dev.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #398      +/-   ##
==========================================
+ Coverage   85.67%   86.10%   +0.42%     
==========================================
  Files          89       97       +8     
  Lines        2101     2792     +691     
==========================================
+ Hits         1800     2404     +604     
- Misses        301      388      +87     
Files Coverage Δ
src/airflow/dags/common_airflow.py 90.38% <100.00%> (ø)
src/airflow/dags/dag_preprocess.py 100.00% <ø> (ø)
src/airflow/dags/finngen_preprocess.py 100.00% <100.00%> (ø)
src/airflow/dags/gwas_curation_update.py 100.00% <100.00%> (ø)
src/gentropy/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/data/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/schemas/__init__.py 100.00% <ø> (ø)
src/gentropy/cli.py 91.66% <100.00%> (ø)
src/gentropy/common/Liftover.py 80.64% <ø> (ø)
... and 75 more

... and 26 files with indirect coverage changes

@d0choa d0choa changed the title feat: susie method feat(fine mapping): susie method Jan 22, 2024
@d0choa d0choa changed the title feat(fine mapping): susie method feat(finemapping): susie method Jan 22, 2024
@ireneisdoomed ireneisdoomed self-requested a review February 5, 2024 10:21
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@d0choa d0choa left a comment

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I think it's good to go. We'll see how things go once we start using the method.
@Daniel-Considine feel free to merge when you are ready

@Daniel-Considine Daniel-Considine merged commit fd9a75e into dev Feb 8, 2024
4 checks passed
@Daniel-Considine Daniel-Considine deleted the dc_susie_method branch February 8, 2024 11:12
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4 participants