org.seqdoop.hadoop_bam.util

Class BGZFCodec

java.lang.Object

org.apache.hadoop.io.compress.DefaultCodec

org.apache.hadoop.io.compress.GzipCodec

org.seqdoop.hadoop_bam.util.BGZFCodec

All Implemented Interfaces:

org.apache.hadoop.conf.Configurable, org.apache.hadoop.io.compress.CompressionCodec, org.apache.hadoop.io.compress.SplittableCompressionCodec

public class BGZFCodec
extends org.apache.hadoop.io.compress.GzipCodec
implements org.apache.hadoop.io.compress.SplittableCompressionCodec

A Hadoop CompressionCodec for the BGZF compression format, which reads and writes files with a .bgz suffix. There is no standard suffix for BGZF-compressed files, and in fact .gz is commonly used, in which case BGZFEnhancedGzipCodec should be used instead of this class.

To use BGZFCodec, set it on the configuration object as follows.

conf.set("io.compression.codecs", BGZFCodec.class.getCanonicalName())

See Also:

BGZFEnhancedGzipCodec

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.io.compress.GzipCodec

org.apache.hadoop.io.compress.GzipCodec.GzipOutputStream

Nested classes/interfaces inherited from interface org.apache.hadoop.io.compress.SplittableCompressionCodec

org.apache.hadoop.io.compress.SplittableCompressionCodec.READ_MODE

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_EXTENSION

Constructor Summary

Constructors

Constructor and Description
BGZFCodec()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.io.compress.Compressor	createCompressor()
org.apache.hadoop.io.compress.SplitCompressionInputStream	createInputStream(InputStream seekableIn, org.apache.hadoop.io.compress.Decompressor decompressor, long start, long end, org.apache.hadoop.io.compress.SplittableCompressionCodec.READ_MODE readMode)
org.apache.hadoop.io.compress.CompressionOutputStream	createOutputStream(OutputStream out)
org.apache.hadoop.io.compress.CompressionOutputStream	createOutputStream(OutputStream out, org.apache.hadoop.io.compress.Compressor compressor)
Class<? extends org.apache.hadoop.io.compress.Compressor>	getCompressorType()
String	getDefaultExtension()

Methods inherited from class org.apache.hadoop.io.compress.GzipCodec

createDecompressor, createInputStream, createInputStream, getDecompressorType

Methods inherited from class org.apache.hadoop.io.compress.DefaultCodec

getConf, setConf

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.apache.hadoop.io.compress.CompressionCodec

createDecompressor, createInputStream, createInputStream, getDecompressorType

Field Detail

DEFAULT_EXTENSION

public static final String DEFAULT_EXTENSION

See Also:

Constant Field Values

Constructor Detail

BGZFCodec

public BGZFCodec()

Method Detail

createOutputStream

public org.apache.hadoop.io.compress.CompressionOutputStream createOutputStream(OutputStream out)
                                                                         throws IOException

Specified by:

createOutputStream in interface org.apache.hadoop.io.compress.CompressionCodec

Overrides:

createOutputStream in class org.apache.hadoop.io.compress.GzipCodec

Throws:

IOException

createOutputStream

public org.apache.hadoop.io.compress.CompressionOutputStream createOutputStream(OutputStream out,
                                                                                org.apache.hadoop.io.compress.Compressor compressor)
                                                                         throws IOException

Specified by:

createOutputStream in interface org.apache.hadoop.io.compress.CompressionCodec

Overrides:

createOutputStream in class org.apache.hadoop.io.compress.GzipCodec

Throws:

IOException

getCompressorType

public Class<? extends org.apache.hadoop.io.compress.Compressor> getCompressorType()

Specified by:

getCompressorType in interface org.apache.hadoop.io.compress.CompressionCodec

Overrides:

getCompressorType in class org.apache.hadoop.io.compress.GzipCodec

createCompressor

public org.apache.hadoop.io.compress.Compressor createCompressor()

Specified by:

createCompressor in interface org.apache.hadoop.io.compress.CompressionCodec

Overrides:

createCompressor in class org.apache.hadoop.io.compress.GzipCodec

createInputStream

public org.apache.hadoop.io.compress.SplitCompressionInputStream createInputStream(InputStream seekableIn,
                                                                                   org.apache.hadoop.io.compress.Decompressor decompressor,
                                                                                   long start,
                                                                                   long end,
                                                                                   org.apache.hadoop.io.compress.SplittableCompressionCodec.READ_MODE readMode)
                                                                            throws IOException

Specified by:

createInputStream in interface org.apache.hadoop.io.compress.SplittableCompressionCodec

Throws:

IOException

getDefaultExtension

public String getDefaultExtension()

Specified by:

getDefaultExtension in interface org.apache.hadoop.io.compress.CompressionCodec

Overrides:

getDefaultExtension in class org.apache.hadoop.io.compress.GzipCodec