blbutil

Class BGZIPOutputStream

java.lang.Object

java.io.OutputStream

blbutil.BGZIPOutputStream

All Implemented Interfaces:

java.io.Closeable, java.io.Flushable, java.lang.AutoCloseable

public final class BGZIPOutputStream
extends java.io.OutputStream

Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.

The GZIP file format specification is described RFC 1952 and the BGZIP file format specification is described in the Sequence Alignment/Map Format Specification

Instances of class BGZIPOutputStream are not thread safe.

Constructor Summary

Constructors

Constructor and Description
BGZIPOutputStream(java.io.OutputStream os, boolean writeEmptyBlock) Creates a new BGZIPOutputStream instance that writes to the specified output stream.

Method Summary

Modifier and Type	Method and Description
void	close()
void	flush()
static void	main(java.lang.String[] args) Applies BGZIP compression on the specified files.
void	write(byte[] ba)
void	write(byte[] buf, int off, int len)
void	write(int b)

Methods inherited from class java.lang.Object

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

Constructor Detail

BGZIPOutputStream

public BGZIPOutputStream(java.io.OutputStream os,
                         boolean writeEmptyBlock)

Creates a new BGZIPOutputStream instance that writes to the specified output stream.

Parameters:

os - the output stream

writeEmptyBlock - true if the close() method will write an empty BGZIP block to the end of the stream

Throws:

java.lang.NullPointerException - if os == null

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException

Applies BGZIP compression on the specified files. The filename of each compressed file will be the original filename followed by ".gz". The original files are not deleted or overwritten. The program exits with an error message if any input filename ends with ".gz".

Parameters:

args - a list of files that will be compressed

Throws:

java.io.IOException - if an I/O error occurs

write

public void write(int b)
           throws java.io.IOException

Specified by:

write in class java.io.OutputStream

Throws:

java.io.IOException

write

public void write(byte[] ba)
           throws java.io.IOException

Overrides:

write in class java.io.OutputStream

Throws:

java.io.IOException

write

public void write(byte[] buf,
                  int off,
                  int len)
           throws java.io.IOException

Overrides:

write in class java.io.OutputStream

Throws:

java.io.IOException

flush

public void flush()
           throws java.io.IOException

Specified by:

flush in interface java.io.Flushable

Overrides:

flush in class java.io.OutputStream

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.OutputStream

Throws:

java.io.IOException