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Issue/237#241

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NickEdwards7502 wants to merge 53 commits intodevaehrc/VariantSpark:devfrom issue/237aehrc/VariantSpark:issue/237Copy head branch name to clipboard

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Commits on Sep 11, 2024

• DEV: Created standalone class for Random Forest Models (#237)

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• DEV: Updated varspark python wrapper (#237)

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• DEV: Created standalone FeatureSource class in separate file (#237)

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• REFACTOR: Remove unecessary hail import for hail rf wrapper

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• DEV: Created standalone ImportanceAnalysis class in

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• DEV: Updated ImportanceAnalysis scala class (#237)

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• DEV: Created scala function that trains a forest

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• REFACTOR: Removed model definition and training

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• DEV: Create no-hail equivalent of JSON model export (#237)

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• REFACTOR: Update importance API test cases to reflect changes (#237)

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• REFACTOR: Update reproducibility test case to reflect changes (#237)

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• DEV: Update python unit testing (#237)

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• DEV: Create no hail lfdr class (#237)

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• DEV: Create temp hail notebook for testing JSON export OOM (#237)

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• DEV: Create temp notebook for demonstrating VS functionality

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Commits on Sep 13, 2024

• DEV: Add covariate import wrapper function (#237)

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• DEV: Create python class for covariate imports (#237)

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• STYLE: Format with black (#237)

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Commits on Sep 19, 2024

• REFACTOR: Remove covariatesource as not required (#237)

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• STYLE: Format with black (#237)

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• DEV: Add wrapper functions for covariate support (#237)

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• STYLE: Format with black (#237)

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• STYLE: Format with black (#237)

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• DEV: Update lfdr to support covariates (#237)

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• STYLE: Format with scalamft (#237)

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• DEV: Update VSContext to support covariates (#237)

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• DEV: Update std CSV features to support optional variable type specs (#237)

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• DEV: Create class for returning union of features and covariates (#237)

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• CHORE: Add reproducibility test that includes covariates (#237)

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• CHORE: Remove print statements from RF reproducibility test (#237)

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• CHORE: Update no hail notebook to include covariates (#237)

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• DEV: Update fdr estimation to return p-value cutoff (#237)

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• FIX: Correct significance line plot to use cutoff p-value (#237)

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• REFACTOR: Update pairwise operation tests based on import changes (#237)

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• CHORE: Update nohail notebook with significance line changes (#237)

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• FIX: Add covariate type parameter to python wrapper for std csv (#237)

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• DEV: Replace to_df functionality with head (#237)

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• DEV: Update FeatureSource dataframe conversion (#237)

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• CHORE: Update nohail demo to include df slicing (#237)

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Commits on Sep 20, 2024

• REFACTOR: Make ExportModel compatible with JsonRFAnalyser (#237)

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Commits on Sep 23, 2024

• REFACTOR: Make head concrete & inherited by all feature sources (#237)

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• FIX: Update regex import for lfdr DataFrame parsing(#237)

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Commits on Oct 2, 2024

• CHORE: Remove cutoff pvalue print statement (#237)

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• CHORE: Remove VSHail python wrapper files (#237)

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• CHORE: Remove VSHail Random Forest scala class (#237)

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• CHORE: Update spark context test to use non-hail Kryo registrator (#237)

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• CHORE: Remove test cases specifically for hail (#237)

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• CHORE: Remove hail from maven build (#237)

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• REFACTOR: Update lfdr filename and python wrapper reference (#237)

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• CHORE: Remove hail unit tests (#237)

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Commits on Oct 17, 2024

• FIX: Update LocalFDR import statement in rfmodel.py (#237)

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• DEV: Integrate bgzipped file support in VCF import API (#237)

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• DEV: Implement imputation for VCF features (#237)

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