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Feature/refactor#85

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lthp wants to merge 21 commits intodevelopmentratschlab/immunopepper:developmentfrom feature/refactorratschlab/immunopepper:feature/refactorCopy head branch name to clipboard

+898-1,012

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Commits on Aug 30, 2023

• added the filter cancer usecase for development

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  771a280

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• refactor cancerspecif

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  2497a4a

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• created a preprocess generic function for preprocess

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  3f44041

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• create input to mode function

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  8abfd51

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• output path naming function

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  167ea52

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• feature: optional removal of normals

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  d20f027

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• cleaning

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• feature: cancer matrix with all samples pre-processed first

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• feature: allow the processing of all cancer samples without filtering individual sample. Large scale changes

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• feature: make restrict the background to the kmers present in the foreground. #TODO kmers solely in annotation

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Commits on Aug 31, 2023

• feature: make restrict the background to the kmers present in the foreground. fix

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Commits on Sep 7, 2023

• output path naming function. fix

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• feature: allow the processing of all cancer samples without filtering individual sample. fixing variable name

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  e595397

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• feature: allow the processing of all cancer samples without filtering individual sample. fixing mutation mode

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  a6c9b21

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Commits on Sep 19, 2023

• minor mutation mode change

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  2bc73b9

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Commits on Oct 26, 2023

• fix indentation

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  d381d8d

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Commits on Oct 31, 2023

• parsers: remove deprecated argument

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  4af8eb5

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• replace main parser with readthedoc compatible version

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  e14a1d4

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• update readthedocs configuration

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  dd373d4

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• correct typo

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  3b2786e

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Commits on Nov 22, 2023

• pepquery wrapper: correct issue in paths declaration

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