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Ac updates #119

Merged
merged 24 commits into from
Apr 1, 2024
Merged

Ac updates #119

merged 24 commits into from
Apr 1, 2024

Commits on Apr 1, 2024

  1. have removed cgat/SequencePairProperties.py to simplify dependancies

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    Acribbs committed Apr 1, 2024
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  2. removed cgat2rdf to make repo easier to maintain

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  3. have updated numpy and pandas to specify correct float and int to sat… 

    …isfy deprication of .int and .float
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    Acribbs committed Apr 1, 2024
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  4. have removed WrapperCodeML because I have no idea what it does so tha… 

    …t we can reduce the amount of code to support
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  5. have removed WrapperCodeML documentation too

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    Acribbs committed Apr 1, 2024
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  6. added import tests to github actions

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    Acribbs committed Apr 1, 2024
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  7. updated tests for unstrip, md5sum is different but output looks the s… 

    …ame. Might be because of the change in float to .float64 and .int64
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    Acribbs committed Apr 1, 2024
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  8. fix github actions yml

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    Acribbs committed Apr 1, 2024
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  9. updated test for unstrip as updated old one

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    Acribbs committed Apr 1, 2024
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  10. added new test for bam2bam set-nh as output is different md5sum but c… 

    …ontent looks the same, likely due to the float and int changes
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  11. updated downsample paired, looks like same output but likely because … 

    …of .int and .float changes in numpy
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    Acribbs committed Apr 1, 2024
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  12. updated downsample single tests, likely related to .int and .float ch… 

    …anges in numpy
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  13. updated bamfiltered because of .int and .float changes

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  14. updated set sequence because of int and float changes in numpy

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  15. updated strip_match to reflect changes in the float and int

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    Acribbs committed Apr 1, 2024
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  16. updated strip_sequence

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    Acribbs committed Apr 1, 2024
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  17. updated strip quality

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    Acribbs committed Apr 1, 2024
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  18. updated unset mapq

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  19. updated unset mapq

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    Acribbs committed Apr 1, 2024
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  20. import of cnested list is not working during github testing, but is l… 

    …ocally, have removed nosetests for imports for the moment
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    Acribbs committed Apr 1, 2024
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  21. modified setup from setup.py to pip

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    Acribbs committed Apr 1, 2024
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  22. update geneprofile as np floats wrong

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    Acribbs committed Apr 1, 2024
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  23. update dnumpy floats

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  24. have removed csv2db as its in cgatcore and imports this as a module a… 

    …nd not used in other code in this repo
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    Acribbs committed Apr 1, 2024
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