org.dishevelled.compress

Class BgzfUtils

java.lang.Object

org.dishevelled.compress.BgzfUtils

public abstract class BgzfUtils
extends Object

Utility code for the block compressed gzip (BGZF) compression format.

Since:

1.3

Author:

Michael Heuer

Method Summary

Modifier and Type	Method and Description
static String	getCompressedFilename(String filename) Maps the given filename to the name that the file should have after compression with block compressed gzip (BGZF).
static String	getUncompressedFilename(String filename) Maps the given name of a block compressed gzip (BGZF) file to the name that the file should have after uncompression.
static boolean	isCompressedFilename(String filename) Detects common block compressed gzip (BGZF) suffixes in the given filename.

Methods inherited from class java.lang.Object

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

Method Detail

isCompressedFilename

public static boolean isCompressedFilename(String filename)

Detects common block compressed gzip (BGZF) suffixes in the given filename.

Parameters:

filename - name of a file

Returns:

true if the filename has a common block compressed gzip (BGZF) suffix, false otherwise

getUncompressedFilename

public static String getUncompressedFilename(String filename)

Maps the given name of a block compressed gzip (BGZF) file to the name that the file should have after uncompression. Commonly used file type specific suffixes like ".bgz" or ".bgzf" are automatically detected and correctly mapped. Any filenames with the generic ".bgz" suffix (or any other generic bgzf suffix) is mapped to a name without that suffix. If no bgzf suffix is detected, then the filename is returned unmapped.

Parameters:

filename - name of a file

Returns:

name of the corresponding uncompressed file

getCompressedFilename

public static String getCompressedFilename(String filename)

Maps the given filename to the name that the file should have after compression with block compressed gzip (BGZF). Currently this method simply appends the suffix ".bgz" to the filename, but a future version may implement a more complex mapping if a new widely used naming pattern emerges.

Parameters:

filename - name of a file

Returns:

name of the corresponding compressed file