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Major PR refactoring the code and making it easily to read / reuse for processing - #2

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ypriverol wants to merge 37 commits into
QuantitativeBiology:mainfrom
bigbio:main
Open

Major PR refactoring the code and making it easily to read / reuse for processing#2
ypriverol wants to merge 37 commits into
QuantitativeBiology:mainfrom
bigbio:main

Merge pull request #6 from bigbio/dev

b8f91cb
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