Package org.monarchinitiative.lirical.background

Class BackgroundFrequencyCommand

java.lang.Object

org.monarchinitiative.lirical.background.BackgroundFrequencyCommand

All Implemented Interfaces:

Callable<Integer>

public class BackgroundFrequencyCommand
extends Object
implements Callable<Integer>

This command is used to generate the background frequency files. It is not needed to run LIRICAL on exome/genome data, but may be interesting for those who desire to use a population frequency data source other than gnomAD. The heavy lifting is done by GenicIntoleranceCalculator. To run the command enter

     java -jar LIRICAL.jar gt2git -e  -g 
 

Author:

Peter Robinson

Field Summary

Fields

Modifier and Type	Field	Description
protected TranscriptDatabase	transcriptDb

Constructor Summary

Constructors

Constructor	Description
BackgroundFrequencyCommand()

Method Summary

Modifier and Type	Method	Description
Integer	call()

Methods inherited from class java.lang.Object

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

Field Details

transcriptDb

protected TranscriptDatabase transcriptDb

Constructor Details

BackgroundFrequencyCommand

public BackgroundFrequencyCommand()

Method Details

call

public Integer call()
             throws LiricalException

Specified by:

call in interface Callable<Integer>

Throws:

LiricalException