Package task

Class ExecutorExpand

java.lang.Object

task.ExecutorExpand

public class ExecutorExpand
extends Object

The ExecutorExpand class is responsible for executing the expand task to extend existing genomic data.

This class orchestrates the process of expanding an existing storage with new variant call files (VCF), updating sample attributes, annotating variants, inferring sequence types, and recomputing statistics.

Constructor Summary

Constructors

Constructor	Description
ExecutorExpand(CLIExpand cli)	Constructs an instance of the ExecutorExpand class.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Details

ExecutorExpand

public ExecutorExpand(CLIExpand cli)
               throws IOException

Constructs an instance of the ExecutorExpand class.

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

• Storage for genomic data, created based on the command-line interface (CLI) input.
• A StorageUpdater to manage updates to the storage.
• A VariantAnnotator to annotate genetic variants.

Parameters:

cli - The CLIExpand 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 IOException,
MusialException

Executes the main logic of the expand task.

This method performs the following steps:

• Processes VCF files to load variants into the storage.
• Reloads existing variant calls from the storage.
• Detaches samples already present in the storage to avoid duplication.
• Updates variants and sample attributes based on the processed VCF data.
• Determines the output path for writing the updated storage data.
• Runs variant annotation using SnpEff if applicable.
• Performs sequence typing if reference sequences are available.
• Recomputes statistics for the storage.
• Writes the updated storage data to the specified output file or logs the changes in dry-run mode.

Throws:

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

MusialException - If an error specific to the application logic occurs.