org.seqdoop.hadoop_bam.util

Class BGZFEnhancedGzipCodec

java.lang.Object

org.apache.hadoop.io.compress.DefaultCodec

org.apache.hadoop.io.compress.GzipCodec

org.seqdoop.hadoop_bam.util.BGZFEnhancedGzipCodec

All Implemented Interfaces:

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

public class BGZFEnhancedGzipCodec
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 .gz suffix.

BGZF is a splittable extension of gzip, which means that all BGZF files are standard gzip files, however the reverse is not necessarily the case. BGZF files often have the standard .gz suffix (such as those produced by the bcftools command), which causes a difficulty since it is not immediately apparent from the filename alone whether a file is a BGZF file, or merely a regular gzip file. BGZFEnhancedGzipCodec will read the start of the file to look for BGZF headers to detect the type of compression.

BGZFEnhancedGzipCodec will read BGZF or gzip files, but currently always writes regular gzip files.

To use BGZFEnhancedGzipCodec, set it on the configuration object as follows. This will override the built-in GzipCodec that is mapped to the .gz suffix.

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

See Also:

BGZFCodec

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

Constructor Summary

Constructors

Constructor and Description
BGZFEnhancedGzipCodec()

Method Summary

Modifier and Type	Method and Description
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)

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

createCompressor, createDecompressor, createInputStream, createInputStream, createOutputStream, createOutputStream, getCompressorType, getDecompressorType, getDefaultExtension

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

createCompressor, createDecompressor, createInputStream, createInputStream, createOutputStream, createOutputStream, getCompressorType, getDecompressorType, getDefaultExtension

Constructor Detail

BGZFEnhancedGzipCodec

public BGZFEnhancedGzipCodec()

Method Detail

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