org.dishevelled.bio.tools

Class AbstractRenameReferences

java.lang.Object

org.dishevelled.bio.tools.AbstractRenameReferences

All Implemented Interfaces:

Callable<Integer>

Direct Known Subclasses:

RenameBedReferences, RenameGff3References, RenameVcfReferences

abstract class AbstractRenameReferences
extends Object
implements Callable<Integer>

Abstract rename references callable.

Author:

Michael Heuer

Field Summary

Fields

Modifier and Type	Field and Description
protected Path	inputPath
protected File	outputFile

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractRenameReferences(boolean chr, Path inputPath, File outputFile) Create a new rename references callable.

Method Summary

Modifier and Type	Method and Description
protected static String	addChr(String referenceName) Add "chr" to the specified reference name.
protected static String	removeChr(String referenceName) Remove "chr" from the specified reference name.
protected String	rename(String referenceName) Rename the specified reference name.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.concurrent.Callable

call

Field Detail

inputPath

protected final Path inputPath

outputFile

protected final File outputFile

Constructor Detail

AbstractRenameReferences

protected AbstractRenameReferences(boolean chr,
                                   Path inputPath,
                                   File outputFile)

Create a new rename references callable.

Parameters:

chr - true to add "chr" to chromosome names

inputPath - input path, if any

outputFile - output file, if any

Method Detail

addChr

protected static String addChr(String referenceName)

Add "chr" to the specified reference name.

Parameters:

referenceName - reference name

Returns:

the specified reference name with "chr" added, with various workarounds for sex and mitochondrial chromosomes

removeChr

protected static String removeChr(String referenceName)

Remove "chr" from the specified reference name.

Parameters:

referenceName - reference name

Returns:

the specified reference name with "chr" removed, with various workarounds for sex and autosomal chromosomes, unplaced contigs, and misversioned reference names

rename

protected String rename(String referenceName)

Rename the specified reference name.

Parameters:

referenceName - reference name, if any

Returns:

the specified reference name with "chr" added or removed