org.dishevelled.bio.tools

Class RenameBedReferences

java.lang.Object

org.dishevelled.bio.tools.AbstractRenameReferences

org.dishevelled.bio.tools.RenameBedReferences

All Implemented Interfaces:

Callable<Integer>

public final class RenameBedReferences
extends AbstractRenameReferences

Rename references in BED 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
RenameBedReferences(boolean chr, File inputBedFile, File outputBedFile) Rename references in BED files.
RenameBedReferences(boolean chr, Path inputBedPath, File outputBedFile) Rename references in BED 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

RenameBedReferences

public RenameBedReferences(boolean chr,
                           File inputBedFile,
                           File outputBedFile)

Rename references in BED files.

Parameters:

chr - true to add "chr" to chromosome names

inputBedFile - input BED file, if any

outputBedFile - output BED file, if any

RenameBedReferences

public RenameBedReferences(boolean chr,
                           Path inputBedPath,
                           File outputBedFile)

Rename references in BED files.

Parameters:

chr - true to add "chr" to chromosome names

inputBedPath - input BED path, if any

outputBedFile - output BED 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