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Refactor SNP frequencies#490

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alimanfoo merged 25 commits intomalariagen:masterfrom
alimanfoo:refactor-snp-frq-2023-12-20
Jan 3, 2024
Merged

Refactor SNP frequencies#490
alimanfoo merged 25 commits intomalariagen:masterfrom
alimanfoo:refactor-snp-frq-2023-12-20

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@alimanfoo alimanfoo commented Dec 20, 2023

Continuing on the journey towards #366 here we refactor functions related to SNP allele frequencies analysis.

Also fix a bug in aa_allele_frequencies() where frequencies would be reported as 0 even where all genotypes are missing, should be nan instead.

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codecov bot commented Dec 20, 2023

Codecov Report

Attention: Patch coverage is 98.64341% with 7 lines in your changes missing coverage. Please review.

Project coverage is 98.59%. Comparing base (7995a0f) to head (3385390).
Report is 427 commits behind head on master.

Files with missing lines Patch % Lines
malariagen_data/anoph/snp_frq.py 98.42% 7 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #490      +/-   ##
==========================================
+ Coverage   98.49%   98.59%   +0.10%     
==========================================
  Files          30       31       +1     
  Lines        2520     2996     +476     
==========================================
+ Hits         2482     2954     +472     
- Misses         38       42       +4     

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@alimanfoo alimanfoo marked this pull request as ready for review January 3, 2024 16:57
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Alright, think I'm just about done here. Planning to merge if CI looks good.

@alimanfoo alimanfoo mentioned this pull request Jan 3, 2024
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@alimanfoo alimanfoo merged commit f4c263f into malariagen:master Jan 3, 2024
@alimanfoo alimanfoo deleted the refactor-snp-frq-2023-12-20 branch January 3, 2024 19:06
@alimanfoo alimanfoo added the BMGF-001927 Work supported by BMGF grant INV-001927 (MalariaGEN 2019-2024). label Dec 4, 2024
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