Package task

Class ExecutorBuild

java.lang.Object

task.ExecutorBuild

public class ExecutorBuild
extends Object

The ExecutorBuild class is responsible for executing the build task to compile genomic data.

This class orchestrates the process of loading genomic features, processing variant call files (VCF), annotating variants, inferring sequence types, and computing statistics.

Constructor Summary

Constructors

Constructor	Description
ExecutorBuild(CLIBuild cli)	Constructs an instance of the ExecutorBuild class.

Method Summary

Modifier and Type	Method	Description
void	run()	Executes the main logic of the build task.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ExecutorBuild

public ExecutorBuild(CLIBuild cli)
              throws IOException

Constructs an instance of the ExecutorBuild class.

This constructor initializes the necessary components for the build task, including:

• Storage for genomic data, created based on the command-line interface (CLI) input.
• A StorageUpdater to manage updates to the storage.
• A FeatureLoader to load and validate genomic features.
• A VCFProcessor to process variant call files (VCF).
• A VariantAnnotator to annotate genetic variants.

Parameters:

cli - The CLIBuild instance containing the command-line arguments and options.

Throws:

IOException - If an I/O error occurs during the initialization of storage or other components.

Method Details

run

public void run()
         throws MusialException,
IOException

Executes the main logic of the build task.

This method performs the following steps:

• Loads and validates genomic features from the input files.
• Processes VCF files to load variant calls into the storage.
• Runs variant annotation using SnpEff if applicable.
• Infers sequence types if reference sequences are available.
• Computes statistics for the genomic data in the storage.
• Writes the processed storage data to the specified output file.

Throws:

MusialException - If an error occurs during the processing of genomic data.

IOException - If an I/O error occurs during file operations.