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malariagen / malariagen-data-python

Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
14 stars 24 forks source link

Improve performance when accessing biallelic SNP calls #623

Closed alimanfoo closed 1 month ago

alimanfoo commented 2 months ago

This PR improves performance of the Anopheles biallelic_snp_calls() function by around an order of magnitude.

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codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 95.64%. Comparing base (80820f3) to head (7929915). Report is 31 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #623 +/- ## ========================================== - Coverage 95.69% 95.64% -0.05% ========================================== Files 39 39 Lines 3853 3904 +51 ========================================== + Hits 3687 3734 +47 - Misses 166 170 +4 ``` | [Flag](https://app.codecov.io/gh/malariagen/malariagen-data-python/pull/623/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=malariagen) | Coverage Δ | | |---|---|---| | [](https://app.codecov.io/gh/malariagen/malariagen-data-python/pull/623/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=malariagen) | `95.64% <100.00%> (?)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=malariagen#carryforward-flags-in-the-pull-request-comment) to find out more.

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