org.dishevelled.bio.tools

Class RenameGff3References

java.lang.Object

org.dishevelled.bio.tools.AbstractRenameReferences

org.dishevelled.bio.tools.RenameGff3References

All Implemented Interfaces:

Callable<Integer>

public final class RenameGff3References
extends AbstractRenameReferences

Rename references in GFF3 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
RenameGff3References(boolean chr, File inputGff3File, File outputGff3File) Rename references in GFF3 files.
RenameGff3References(boolean chr, Path inputGff3Path, File outputGff3File) Rename references in GFF3 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

RenameGff3References

public RenameGff3References(boolean chr,
                            File inputGff3File,
                            File outputGff3File)

Rename references in GFF3 files.

Parameters:

chr - true to add "chr" to chromosome names

inputGff3File - input GFF3 file, if any

outputGff3File - output GFF3 file, if any

RenameGff3References

public RenameGff3References(boolean chr,
                            Path inputGff3Path,
                            File outputGff3File)

Rename references in GFF3 files.

Parameters:

chr - true to add "chr" to chromosome names

inputGff3Path - input GFF3 path, if any

outputGff3File - output GFF3 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