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Refactor combine_scorefiles #62

Merged
merged 41 commits into from
Dec 15, 2023
Merged

Refactor combine_scorefiles #62

merged 41 commits into from
Dec 15, 2023

Commits on Oct 30, 2023

  1. draft streaming with generators

    @nebfield
    nebfield committed Oct 30, 2023
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  2. set up effect types

    @nebfield
    nebfield committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. profiling improvements

    @nebfield
    nebfield committed Oct 31, 2023
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  2. fix output

    @nebfield
    nebfield committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. check for duplicates

    @nebfield
    nebfield committed Nov 1, 2023
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  2. add liftover

    @nebfield
    nebfield committed Nov 1, 2023
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  3. update dependencies and set up pre-commit

    @nebfield
    nebfield committed Nov 1, 2023
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  4. complain when linting fails

    @nebfield
    nebfield committed Nov 1, 2023
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  5. fix linting

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    nebfield committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. support wide files

    @nebfield
    nebfield committed Nov 2, 2023
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  2. add log

    @nebfield
    nebfield committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. fix tests and liftover

    @nebfield
    nebfield committed Nov 3, 2023
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  2. fix test

    @nebfield
    nebfield committed Nov 3, 2023
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  3. sqlite support and add log data

    @nebfield
    nebfield committed Nov 3, 2023
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Commits on Nov 6, 2023

  1. fix tests

    @nebfield
    nebfield committed Nov 6, 2023
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  2. fix tests

    @nebfield
    nebfield committed Nov 6, 2023
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  3. fixes to make old and new output consistent

    @nebfield
    nebfield committed Nov 6, 2023
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  4. update tests

    @nebfield
    nebfield committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. drop parallel gzip and --threads

    @nebfield
    nebfield committed Nov 7, 2023
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Commits on Nov 16, 2023

  1. create ScoreVariant and EffectType classes

    @nebfield
    nebfield committed Nov 16, 2023
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  2. review comments

    @nebfield
    nebfield committed Nov 16, 2023
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  3. add type hints

    @nebfield
    nebfield committed Nov 16, 2023
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  4. remove coordinates from mandatory fields

    @nebfield
    nebfield committed Nov 16, 2023
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Commits on Nov 20, 2023

  1. fix old scoring files

    @nebfield
    nebfield committed Nov 20, 2023
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  2. check effect alleles and compelx scoring files

    @nebfield
    nebfield committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. don't access __annotations__ directly

    @nebfield
    nebfield committed Nov 21, 2023
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  2. remove logger

    @nebfield
    nebfield committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. warn about complex files and variant mismatch

    @nebfield
    nebfield committed Nov 22, 2023
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Commits on Dec 6, 2023

  1. refactor scorevariant from userdict to class with __slots__

    @nebfield
    nebfield committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. fix __repr__ and type hints

    @nebfield
    nebfield committed Dec 7, 2023
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Commits on Dec 11, 2023

  1. add pyarrow support

    @nebfield
    nebfield committed Dec 11, 2023
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Commits on Dec 13, 2023

  1. add license data to log

    @nebfield
    nebfield committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. add custom exceptions

    @nebfield
    nebfield committed Dec 14, 2023
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  2. add custom exit code

    @nebfield
    nebfield committed Dec 14, 2023
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  3. move class definitions

    @nebfield
    nebfield committed Dec 14, 2023
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  4. rename

    @nebfield
    nebfield committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. update effect allele class

    @nebfield
    nebfield committed Dec 15, 2023
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  2. tidy up docstring

    @nebfield
    nebfield committed Dec 15, 2023
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  3. add docstrings to pytest

    @nebfield
    nebfield committed Dec 15, 2023
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  4. fix pyproject

    @nebfield
    nebfield committed Dec 15, 2023
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  5. Merge pull request #73 from PGScatalog/exit_codes 

    Add custom exceptions
    @nebfield
    nebfield authored Dec 15, 2023
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