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Local alleles #266

Merged
merged 13 commits into from
Jul 10, 2024
Merged

Local alleles #266

merged 13 commits into from
Jul 10, 2024

Commits on Jul 10, 2024

  1. Add LAA field during explode step

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  2. Add local-alleles option to CLI

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  3. Ensure that LAA always has a three-dimensional shape

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  4. Add more unit tests

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  5. Use NumPy API to compute LAA

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  6. Only compute LAA if not present 

    Only add LAA field if not present
Infer observed alleles from PL field
    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  7. Only add LAA if PL is present

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  8. Simplify can_localize logic

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  9. Simplify compute_laa_field

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  10. Use boolean flag in CLI option

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  11. Add triploid unit test

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  12. Add compute_laa_field description

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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  13. Fix test_du

    @Will-Tyler
    Will-Tyler committed Jul 10, 2024
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