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Create module to filter out aligned reads #13

Merged
merged 22 commits into from
Oct 20, 2023
Merged

Create module to filter out aligned reads #13

merged 22 commits into from
Oct 20, 2023

Commits on Oct 19, 2023

  1. feat: boilerplate for filter_blacklist module [WIP]

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  2. chore: Merge branch 'main' into filter-aligned

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  3. feat: write filter_aligned process and test workflow

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  4. fix: samtools view doesn't output index

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  5. test: create tests for samtools/filter_aligned

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  6. fix: lint errors

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  7. test: custom pytest to check unaligned reads

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  8. feat: index bam

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  9. ci: install from requirements.txt

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  10. fix(test): handle paired & single differently

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  11. fix(test): define workflow_dir

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  12. fix: test md5sums

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  13. chore: remove comments

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  14. chore: add PR #s

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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Commits on Oct 20, 2023

  1. Merge branch 'main' into filter-aligned

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  2. style: prettier changelog

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  3. test: switch to mus musculus test data

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  4. test: switch mouse to human test data -- no genome fasta for mouse

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  5. test: fix md5sums for human test data

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  6. ci: require pysam >= 0.22

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  7. test: simplify test logic

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  8. test: simplify single read test logic

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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