Package task

package task

Implements tasks that represent high-level workflows of the application, each encapsulating a specific sequence of operations.

Each implemented class should be paired with one MusialTask and CLI implementation, and implement a run() method as well as at least a Storage instance as field. Instances of classes implemented in the op (Operations) package should be used to perform the actual atomic operations on the linked Storage instance.

Implemented classes are intended to be initialized in the Musial.main(java.lang.String[]) method.

For example the ExecutorBuild class is responsible for executing the build task, which includes loading genomic features (FeatureLoader), processing variant call files (VCF) (VCFProcessor), annotating variants (VariantAnnotator ), inferring sequence types, and computing statistics (StorageUpdater), and is paired with the MusialTask.BUILD task and CLIBuild CLI implementation.

Classes

Class	Description
ExecutorBuild	The ExecutorBuild class is responsible for executing the build task to compile genomic data.
ExecutorExpand	The ExecutorExpand class is responsible for executing the expand task to extend existing genomic data.
ExecutorProfile	The ExecutorProfile class is responsible for executing the profile task to profile samples.
ExecutorSequence	The ExecutorSequence class is responsible for executing the sequence task to profile samples.
ExecutorView	The ExecutorView class is responsible for executing the view task for inspecting data.