FEAT: Implemented RF class method for fitting the model

FEAT: Implemented RF class method for obtaining importance analysis
from a fitted RF

FEAT: Implemented RF class method for returning oob error

FEAT: Implemented RF class method for obtaining FDR
from a fitted model

FEAT: Implemented RF class method for exporting forest to JSON

REFACTOR: Make RF model available at package level

CHORE: Added type checking to all methods

REFACTOR: Removed FeatureSource and
ImportanceAnalysis classes from core

REFACTOR: Added FeatureSource import so features
can be returned as a class instantiation

REFACTOR: Removed imp analysis and model training

FEAT: Added conversion from feature to RDD (python)

FEAT: Added conversion from feature to RDD (scala)

CHORE: Added type checking

due to import order warning (#237)

separate wrapper file (#237)

REFACTOR: Updated important_variables and variable_importance
methods to convert to pandas DataFrames

REFACTOR: Removed model training from object instantation and
updated class to accept a model as a parameter

REFACTOR: Added normalisation as an optional parameter for
variable importance methods

FEAT: Updated variableImportance method to include splitCount in return as it is required for local FDR analysis

and passes back to python context (#237)

from importAnalysis method of AnalyticsFunctions (#237)

FIX: Update export function to process trees in batches,
instead of collecting the whole forest as a map as this
led to OOM errors on large forests

REFACTOR: Refactor to mirror changes to python wrapper

FEAT: Include FDR calculation in unit test

FEAT: Implement function for manhattan plotting negative log p values

without hail (#237)

STYLE: Format with black

FEAT: Add wrapper class for importing covariates

FEAT: Add wrapper class for unioning features and covariates

REFACTOR: Include covariate filtering in manhattan plot function

STYLE: Format with black (#237)

FEAT: Add functions for importing std and transposed CSVs

FEAT: Add function for unioning features and covariates

…237)

Reference changed to importTransposedCSV

REFACTOR: Remove python component of converting Feature RDD to pandas

FEAT: Add RDD slice to DF function

REFACTOR: Remove conversion of whole RDD to DataFrame

FEAT: Add function for slicing rows and columns and converting to DF

* .bgz loader function implemented by Christina

* Update python wrapper to include imputation strategy parameter

* Update scala API to pass imputation strategy to VCFFeatureSource

* Create functions to handle mode and zero imputation strategies

* Added imputation strategy to test cases

* Added imputation strategy to FeatureSource cli

* Remove sparkPar from test cases due to changes in class signature

* Updated DefVariantToFeatureConverterTest to use zeros imputation