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Add counts to annotated XML generation #371

Merged
merged 20 commits into from
Apr 26, 2023
Merged

Add counts to annotated XML generation #371

merged 20 commits into from
Apr 26, 2023
+580 −47

Commits on Apr 25, 2023

  1. add report of counts to annotated xml

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  2. initialise counts in iter method

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  3. add counts for genes, consequences, and EFO ids already in ClinVar

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  4. add retries to oxo xref fetching

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  5. sort hgvs in repeat expansion pipeline

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  6. add scoring to annotated clinvar

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  7. compute f1 only when both annotations present

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  8. refactor metrics

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  9. reformat Orphanet identifiers for easier comparison

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  10. fix errors in counting

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  11. update expected output

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  12. WIP - mapping genes and xrefs

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  13. fix xref mapping logic, add percentages

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  14. fix test

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  15. cleaning up

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  16. clarify some comments

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  17. fix memory issue

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  18. make uri_to_curie slightly more robust

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  19. address review comments

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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  20. bump pipeline version

    @apriltuesday
    apriltuesday committed Apr 25, 2023
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