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Add Hail-like AC, AN, and AF computation to variant stats V3 #731

Merged
merged 33 commits into from
Aug 2, 2024
Merged

Add Hail-like AC, AN, and AF computation to variant stats V3 #731

merged 33 commits into from
Aug 2, 2024

Commits on Jul 19, 2024

  1. read more fields from variant stats

    @awenocur
    awenocur committed Jul 19, 2024
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  2. make use of V3 additions in variant stats reader, cache non-refs

    @awenocur
    awenocur committed Jul 19, 2024
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  3. make variant stats reader track entering/exiting ref blocks

    @awenocur
    awenocur committed Jul 19, 2024
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  4. fix sorting logic for ref blocks

    @awenocur
    awenocur committed Jul 19, 2024
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  5. update IAF with ref blocks for variant stats V3

    @awenocur
    awenocur committed Jul 19, 2024
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  6. fix AF computation for variant stats V3

    @awenocur
    awenocur committed Jul 19, 2024
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  7. fix data frame cardinality for variant stats reads

    @awenocur
    awenocur committed Jul 19, 2024
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  8. add TILEDB_IAC, TILEDB_IAN to data query

    @awenocur
    awenocur committed Jul 19, 2024
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  9. update variant stats reader for v3, fix variant stats timing

    @awenocur
    awenocur committed Jul 19, 2024
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  10. fix progressive VCF stats computation, update tests

    @awenocur
    awenocur committed Jul 19, 2024
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  11. fix variant stats v3 writer: correct ordering and END

    @awenocur
    awenocur committed Jul 19, 2024
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  12. read in max_length when reading variant stats

    @awenocur
    awenocur committed Jul 19, 2024
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  13. Refactor inclusion/exclusion of positions, add non-ref extension

    @awenocur
    awenocur committed Jul 19, 2024
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  14. info_TILEDB_IAN is pared down to a single encapsulated element

    @awenocur
    awenocur committed Jul 19, 2024
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  15. fix type mismatch

    @awenocur
    awenocur committed Jul 19, 2024
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  16. make tiledb_IAF_IAN a scalar value

    @awenocur
    awenocur committed Jul 19, 2024
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  17. minor fix to comparison

    @awenocur
    awenocur committed Jul 19, 2024
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  18. isolate variant stats v3 feature from v2

    @awenocur
    awenocur committed Jul 19, 2024
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  19. refactored stats v3 writer in-place sorting to include samples

    @awenocur
    awenocur committed Jul 19, 2024
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  20. simplify in-place sort loop in variant stats writer

    @awenocur
    awenocur committed Jul 19, 2024
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  21. clean up extra string comparison

    @awenocur
    awenocur committed Jul 19, 2024
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  22. move AF computation to method file

    @awenocur
    awenocur committed Jul 19, 2024
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  23. variant stats writer sorting fix

    @awenocur
    awenocur committed Jul 19, 2024
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  24. fix IAC/IAF computation error for variant stats v3

    @awenocur
    awenocur committed Jul 19, 2024
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  25. refactor

    @awenocur
    awenocur committed Jul 19, 2024
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  26. fix AF computations

    @awenocur
    awenocur committed Jul 19, 2024
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Commits on Jul 20, 2024

  1. fix test

    @awenocur
    awenocur committed Jul 20, 2024
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Commits on Jul 31, 2024

  1. restructure writer for normalizing alleles

    @awenocur
    awenocur committed Jul 31, 2024
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  2. add normalization for variant stats v3

    @awenocur
    awenocur committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. change normalization of variant stats V3 to pairwise

    @awenocur
    awenocur committed Aug 1, 2024
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  2. reimplement variant stats V3 pairwise normalization, including ref 

    This reverts commit 81eda28.
    @awenocur
    awenocur committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. address nits and add documentation

    @awenocur
    awenocur committed Aug 2, 2024
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  2. non-functional assignment change for variant stats end

    @awenocur
    awenocur committed Aug 2, 2024
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