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Implemented the feature_pipeline wrapper for taking in the raw features and executing the feature transformations on the tensors.

Implemented the main input_pipeline wrapper for executing all ensembled and non-ensembled feature transformations and collecting them appropriately.

Added some miscellaneous feature transformations, as well as some others for fixing and correcting residue types.

Added wrapper DataPipeline class responsible for running the alignment tools and assembling the input features.