Package op

package op

Implements atomic operations building the core functionality of the application.

It encapsulates the operation logic from the higher-level business logic (see main), command-line interface (see cli), and underlying genomic data storage model (see model). This ensures that each operation is as self-contained as possible, can be reused in different contexts, can be tested independently, and the application remains modular and maintainable.

In contrast to static utility methods (see util), operations in this package are implemented as classes that can maintain intermediate processing results and states relevant for logging and modularization. Each implemented class should evolve around a linked Storage instance and provide a public method to execute the operation.

Class	Description
AminoacidSequenceGenerator	The AminoacidSequenceGenerator class is responsible for generating aminoacid sequences based on genomic data contained in a Storage instance.
FeatureLoader	The FeatureLoader class is responsible for loading and validating genomic features.
NucleotideSequenceGenerator	The NucleotideSequenceGenerator class is responsible for generating nucleotide sequences based on genomic data contained in a Storage instance.
SequenceGenerator	Interface for generating sequences based on a sample identifier.
StorageFactory	Factory class for creating and loading Storage objects.
StorageIO	The StorageIO class provides utility methods for serializing and deserializing genomic data.
StorageTable	The StorageTable class provides functionality to create and manage tabular representations of genomic data stored in a Storage instance using the tablesaw library.
StorageUpdater	Encapsulates complex update logic for genomic data storage from the Storage class itself.
VariantAnnotator	The VariantAnnotator class provides functionality to annotate variants.
VCFProcessor	The VCFProcessor class is responsible for processing Variant Call Format (VCF) files.
VCFProcessor.UpstreamDeletion	Represents an upstream deletion affecting a sample.