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malariagen / malariagen-data-python

Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
13 stars 23 forks source link

Refactor SNP frequencies #490

Closed alimanfoo closed 7 months ago

alimanfoo commented 8 months ago

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 8 months ago

Codecov Report

Attention: 7 lines in your changes are missing coverage. Please review.

Comparison is base (7995a0f) 98.49% compared to head (3385390) 98.59%.

Files Patch % Lines
malariagen_data/anoph/snp_frq.py 98.42% 7 Missing :warning:
Additional details and impacted files ```diff @@ 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 commented 7 months ago

Alright, think I'm just about done here. Planning to merge if CI looks good.