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Refactor G123#495

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alimanfoo merged 6 commits intomalariagen:masterfrom
alimanfoo:refactor-g123-2024-01-08
Jan 9, 2024
Merged

Refactor G123#495
alimanfoo merged 6 commits intomalariagen:masterfrom
alimanfoo:refactor-g123-2024-01-08

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@alimanfoo alimanfoo commented Jan 8, 2024

Continuing towards #366, this PR refactors G123 functions into a separate module.

Also fix minor issues with SNP frequencies causing test failures (resolves #491).

@alimanfoo alimanfoo mentioned this pull request Jan 8, 2024
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codecov bot commented Jan 8, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.65%. Comparing base (5a68bd8) to head (b095b40).
Report is 424 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #495      +/-   ##
==========================================
+ Coverage   98.59%   98.65%   +0.06%     
==========================================
  Files          31       32       +1     
  Lines        2996     3133     +137     
==========================================
+ Hits         2954     3091     +137     
  Misses         42       42              

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@alimanfoo alimanfoo marked this pull request as ready for review January 8, 2024 23:09
@alimanfoo alimanfoo merged commit 6f6ca39 into malariagen:master Jan 9, 2024
@alimanfoo alimanfoo deleted the refactor-g123-2024-01-08 branch January 9, 2024 08:53
@alimanfoo alimanfoo added the BMGF-001927 Work supported by BMGF grant INV-001927 (MalariaGEN 2019-2024). label Dec 4, 2024
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BMGF-001927 Work supported by BMGF grant INV-001927 (MalariaGEN 2019-2024).

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Exclude samples with unassigned taxon from advanced allele frequencies cohorts

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