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Replace bedtools sort with unix sort in BEDTOOLS_GENOMECOV #6063

Merged
merged 6 commits into from
Aug 7, 2024
Merged

Replace bedtools sort with unix sort in BEDTOOLS_GENOMECOV #6063

merged 6 commits into from
Aug 7, 2024

Commits on Jul 30, 2024

  1. Replace bedtools sort with unix sort in BEDTOOLS_GENOMECOV 

    `bedtools sort` uses a large amount of CPUs and memory, but when using it here it doesn't require the  additional genome based features of `bedtools`. Replacing it should speed up the process and make it many times more efficient.
    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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  2. add args2 for for customisation of GNU sort command 

    Allows customisation of GNU
    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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  3. quoting for args2

    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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  4. Use LC_ALL and default options for performance and consistency

    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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  5. Handle null memory value

    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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  6. Remove tags.yml

    @adamrtalbot
    adamrtalbot committed Jul 30, 2024
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