htsjdk.samtools.cram.compression

Class ExternalCompression

java.lang.Object

htsjdk.samtools.cram.compression.ExternalCompression

public class ExternalCompression
extends java.lang.Object

Methods to provide CRAM external compression/decompression features.

Constructor Summary

Constructors

Constructor and Description
ExternalCompression()

Method Summary

Modifier and Type	Method and Description
static byte[]	bzip2(byte[] data) Compress a byte array into BZIP2 blob.
static byte[]	gunzip(byte[] data) Uncompress a GZIP data blob into a new byte array.
static byte[]	gzip(byte[] data) Compress a byte array into GZIP blob.
static byte[]	rans(byte[] data, int order) Compress a byte array into rANS blob.
static byte[]	rans(byte[] data, RANS.ORDER order) Compress a byte array into rANS blob.
static byte[]	unbzip2(byte[] data) Uncompress a BZIP2 data blob into a new byte array.
static byte[]	unrans(byte[] data) Uncompress a rANS data blob into a new byte array.
static byte[]	unxz(byte[] data) Uncompress a XZ data blob into a new byte array.
static byte[]	xz(byte[] data) Compress a byte array into XZ blob.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExternalCompression

public ExternalCompression()

Method Detail

gzip

public static byte[] gzip(byte[] data)
                   throws java.io.IOException

Compress a byte array into GZIP blob. The method obeys GZIP_COMPRESSION_LEVEL compression level.

Parameters:

data - byte array to compress

Returns:

compressed blob

Throws:

java.io.IOException

gunzip

public static byte[] gunzip(byte[] data)
                     throws java.io.IOException

Uncompress a GZIP data blob into a new byte array.

Parameters:

data - compressed data blob

Returns:

uncompressed data

Throws:

java.io.IOException - as per java IO contract

bzip2

public static byte[] bzip2(byte[] data)
                    throws java.io.IOException

Compress a byte array into BZIP2 blob.

Parameters:

data - byte array to compress

Returns:

compressed blob

Throws:

java.io.IOException

unbzip2

public static byte[] unbzip2(byte[] data)
                      throws java.io.IOException

Uncompress a BZIP2 data blob into a new byte array.

Parameters:

data - compressed data blob

Returns:

uncompressed data

Throws:

java.io.IOException - as per java IO contract

rans

public static byte[] rans(byte[] data,
                          RANS.ORDER order)

Compress a byte array into rANS blob.

Parameters:

data - byte array to compress

order - rANS order

Returns:

compressed blob

rans

public static byte[] rans(byte[] data,
                          int order)

Compress a byte array into rANS blob.

Parameters:

data - byte array to compress

order - rANS order

Returns:

compressed blob

unrans

public static byte[] unrans(byte[] data)

Uncompress a rANS data blob into a new byte array.

Parameters:

data - compressed data blob

Returns:

uncompressed data

xz

public static byte[] xz(byte[] data)
                 throws java.io.IOException

Compress a byte array into XZ blob.

Parameters:

data - byte array to compress

Returns:

compressed blob

Throws:

java.io.IOException

unxz

public static byte[] unxz(byte[] data)
                   throws java.io.IOException

Uncompress a XZ data blob into a new byte array.

Parameters:

data - compressed data blob

Returns:

uncompressed data

Throws:

java.io.IOException - as per java IO contract