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DI-809 refactor #9

Merged
merged 65 commits into from
Sep 23, 2024
Merged

DI-809 refactor #9

merged 65 commits into from
Sep 23, 2024

Commits on Sep 13, 2024

  1. update dxapp.json

    @jethror1
    jethror1 committed Sep 13, 2024
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  2. remove bedtools tar

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    jethror1 committed Sep 13, 2024
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  3. remove shell script

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    jethror1 committed Sep 13, 2024
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  4. move python app code

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    jethror1 committed Sep 13, 2024
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  5. add .gitignore

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    jethror1 committed Sep 13, 2024
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  6. add functions to get variant counts and calculate ratios

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    jethror1 committed Sep 13, 2024
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  7. formatting

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    jethror1 committed Sep 13, 2024
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  8. more comments

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    jethror1 committed Sep 13, 2024
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  9. remove comment

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    jethror1 committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. update readme

    @jethror1
    jethror1 committed Sep 16, 2024
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  2. fix formatting

    @jethror1
    jethror1 committed Sep 16, 2024
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  3. update readme

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    jethror1 committed Sep 16, 2024
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  4. add uploading of output file

    @jethror1
    jethror1 committed Sep 16, 2024
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  5. add bedtools dependency asset

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    jethror1 committed Sep 16, 2024
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  6. add comments

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    jethror1 committed Sep 16, 2024
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  7. remove default file for bed file

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    jethror1 committed Sep 16, 2024
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  8. add developers and authorizedUsers to dxapp.json

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    jethror1 committed Sep 16, 2024
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  9. add version to dxapp.json

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    jethror1 committed Sep 16, 2024
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  10. update entrypoint in dxapp.json

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    jethror1 committed Sep 16, 2024
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  11. add ubuntu version to dxapp.json

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    jethror1 committed Sep 16, 2024
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Commits on Sep 19, 2024

  1. add rounding

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    jethror1 committed Sep 19, 2024
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  2. update interpreter in dxapp.json

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    jethror1 committed Sep 19, 2024
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  3. actually download the input files

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    jethror1 committed Sep 19, 2024
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  4. update .gitignore

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    jethror1 committed Sep 19, 2024
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  5. add pysam wheel

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    jethror1 committed Sep 19, 2024
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  6. add requirements.txt

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    jethror1 committed Sep 19, 2024
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  7. add test setup

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    jethror1 committed Sep 19, 2024
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  8. skip ref hom sites

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    jethror1 committed Sep 19, 2024
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  9. bonus upload print

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    jethror1 committed Sep 19, 2024
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  10. update pytest workflow

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    jethror1 committed Sep 19, 2024
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  11. start tests

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    jethror1 committed Sep 19, 2024
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  12. update .gitignore

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    jethror1 committed Sep 19, 2024
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  13. update bedtools install

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    jethror1 committed Sep 19, 2024
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  14. update bedtools install

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    jethror1 committed Sep 19, 2024
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  15. update requirement.txt

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    jethror1 committed Sep 19, 2024
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  16. lots of unit tests

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    jethror1 committed Sep 19, 2024
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  17. remove early rounding of aaf

    @jethror1
    jethror1 committed Sep 19, 2024
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  18. add test data

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    jethror1 committed Sep 19, 2024
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  19. update .gitignore

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    jethror1 committed Sep 19, 2024
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  20. update readme

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    jethror1 committed Sep 19, 2024
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  21. remove output file name parameter

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    jethror1 committed Sep 19, 2024
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  22. remove developer readme

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    jethror1 committed Sep 19, 2024
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Commits on Sep 20, 2024

  1. fix return in get_het_hom_counts

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    jethror1 committed Sep 20, 2024
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  2. ensure only autosomes used for calculations

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    jethror1 committed Sep 20, 2024
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  3. add tests for is_autosome

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    jethror1 committed Sep 20, 2024
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  4. update comment

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    jethror1 committed Sep 20, 2024
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  5. improve log of record

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    jethror1 committed Sep 20, 2024
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  6. fix to allow running locally and in DNAnexus

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    jethror1 committed Sep 20, 2024
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  7. fix pep8 issues

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    jethror1 committed Sep 20, 2024
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  8. improve prints

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    jethror1 committed Sep 20, 2024
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  9. add comment

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    jethror1 committed Sep 20, 2024
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  10. update output field help

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    jethror1 committed Sep 20, 2024
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  11. Black reformat

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    jethror1 committed Sep 20, 2024
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  12. remove x var confusion

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    jethror1 committed Sep 20, 2024
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  13. improve logging of variants with missing fields

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    jethror1 committed Sep 20, 2024
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  14. add unit tests for main

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    jethror1 committed Sep 20, 2024
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  15. add empty vcf

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    jethror1 committed Sep 20, 2024
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  16. add additional unit tests for main

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    jethror1 committed Sep 20, 2024
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  17. improve counter

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    jethror1 committed Sep 20, 2024
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  18. separate alt het variants out

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    jethror1 committed Sep 20, 2024
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  19. update readme

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    jethror1 committed Sep 20, 2024
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  20. add alt het variant to test.vcf

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    jethror1 committed Sep 20, 2024
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  21. update tests for alt het variant

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    jethror1 committed Sep 20, 2024
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  22. add tests for skipping variants with missing values

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    jethror1 committed Sep 20, 2024
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  23. fix readme typo

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    jethror1 committed Sep 20, 2024
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