Package htsjdk.samtools.cram.compression
Class ExternalCompression
- java.lang.Object
-
- htsjdk.samtools.cram.compression.ExternalCompression
-
public class ExternalCompression extends Object
Methods to provide CRAM external compression/decompression features.
-
-
Constructor Summary
Constructors Constructor Description ExternalCompression()
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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[]
uncompress(BlockCompressionMethod method, byte[] compressedContent)
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.
-
-
-
Method Detail
-
gzip
public static byte[] gzip(byte[] data) throws IOException
Compress a byte array into GZIP blob. The method obeysGZIP_COMPRESSION_LEVEL
compression level.- Parameters:
data
- byte array to compress- Returns:
- compressed blob
- Throws:
IOException
-
gunzip
public static byte[] gunzip(byte[] data) throws IOException
Uncompress a GZIP data blob into a new byte array.- Parameters:
data
- compressed data blob- Returns:
- uncompressed data
- Throws:
IOException
- as per java IO contract
-
bzip2
public static byte[] bzip2(byte[] data) throws IOException
Compress a byte array into BZIP2 blob.- Parameters:
data
- byte array to compress- Returns:
- compressed blob
- Throws:
IOException
-
unbzip2
public static byte[] unbzip2(byte[] data) throws IOException
Uncompress a BZIP2 data blob into a new byte array.- Parameters:
data
- compressed data blob- Returns:
- uncompressed data
- Throws:
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 compressorder
- 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 compressorder
- 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 IOException
Compress a byte array into XZ blob.- Parameters:
data
- byte array to compress- Returns:
- compressed blob
- Throws:
IOException
-
unxz
public static byte[] unxz(byte[] data) throws IOException
Uncompress a XZ data blob into a new byte array.- Parameters:
data
- compressed data blob- Returns:
- uncompressed data
- Throws:
IOException
- as per java IO contract
-
uncompress
public static byte[] uncompress(BlockCompressionMethod method, byte[] compressedContent)
-
-