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Compute and plot inversion frequencies#1282

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31puneet wants to merge 26 commits into
malariagen:masterfrom
31puneet:652-karyotype-frequencies
Open

Compute and plot inversion frequencies#1282
31puneet wants to merge 26 commits into
malariagen:masterfrom
31puneet:652-karyotype-frequencies

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@31puneet

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This PR introduces the inversion_frequencies to resolve #652, and replace PR #732. I have added the following refactoring and tests to finalize the feature:

  • Implementes inversion_frequencies and inversion_frequencies_advanced analogous to SNP calculations.
  • Added unit tests extending test_inversion_frq.py

@31puneet

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Hi @jonbrenas
Do you suggest any changes over here ?

@jonbrenas jonbrenas left a comment

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If tests are added in test_inversion_frq.py, we don't need the whole test suite in test_ag3.py.

@31puneet

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If tests are added in test_inversion_frq.py, we don't need the whole test suite in test_ag3.py.

Done!

jonbrenas
jonbrenas previously approved these changes Apr 14, 2026
@31puneet 31puneet requested a review from jonbrenas April 22, 2026 05:16
@31puneet

31puneet commented May 4, 2026

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Hi @jonbrenas PTAL

@31puneet

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Hi @jonbrenas, is this PR still okay for merge?

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Hi @31puneet, I am going to give it a new review but the plan is still to merge it in the not too distant future.

Comment thread malariagen_data/anoph/inversion_frq.py Outdated

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LGTM

@31puneet

31puneet commented Jun 2, 2026

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Hi @jonbrenas Could we merge this pr?

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Hi @31puneet. Merging will take place after a discussion (offline) between the code owners.

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Karyotype frequencies

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