org.dishevelled.bio.tools

Class RenameVcfReferences

java.lang.Object

org.dishevelled.bio.tools.AbstractRenameReferences

org.dishevelled.bio.tools.RenameVcfReferences

All Implemented Interfaces:

Callable<Integer>

public final class RenameVcfReferences
extends AbstractRenameReferences

Rename references in VCF files.

Since:

2.1

Author:

Michael Heuer

Field Summary

Fields inherited from class org.dishevelled.bio.tools.AbstractRenameReferences

inputPath, outputFile

Constructor Summary

Constructors

Constructor and Description
RenameVcfReferences(boolean chr, File inputVcfFile, File outputVcfFile) Rename references in VCF files.
RenameVcfReferences(boolean chr, Path inputVcfPath, File outputVcfFile) Rename references in VCF files.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class org.dishevelled.bio.tools.AbstractRenameReferences

addChr, removeChr, rename

Methods inherited from class java.lang.Object

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

Constructor Detail

RenameVcfReferences

public RenameVcfReferences(boolean chr,
                           File inputVcfFile,
                           File outputVcfFile)

Rename references in VCF files.

Parameters:

chr - true to add "chr" to chromosome names

inputVcfFile - input VCF file, if any

outputVcfFile - output VCF file, if any

RenameVcfReferences

public RenameVcfReferences(boolean chr,
                           Path inputVcfPath,
                           File outputVcfFile)

Rename references in VCF files.

Parameters:

chr - true to add "chr" to chromosome names

inputVcfPath - input VCF path, if any

outputVcfFile - output VCF file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args