java.lang.Object

java.io.OutputStream

blbutil.BGZIPOutputStream

All Implemented Interfaces:: Closeable, Flushable, AutoCloseable

public final class BGZIPOutputStream extends 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

Description

BGZIPOutputStream(OutputStream os, boolean writeEmptyBlock)

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

Modifier and Type

Method

Description

void

close()

void

flush()

static void

main(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)

static void

writeEmptyBlock(OutputStream os)

Write an empty BGZIP block to the specified output stream.

Methods inherited from class java.io.OutputStream
nullOutputStream

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- BGZIPOutputStream
  
  public BGZIPOutputStream(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:
  
  NullPointerException - if os == null
Method Details
- main
  
  public static void main(String[] args) throws 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:
  
  IOException - if an I/O error occurs
- writeEmptyBlock
  
  public static void writeEmptyBlock(OutputStream os) throws IOException
  
  Write an empty BGZIP block to the specified output stream. The Java Virtual Machine will exit with an error message if an IOException is thrown while writing the empty BGZIP block.
  
  Parameters:
  
  os - the output stream
  
  Throws:
  
  IOException - if an I/O error occurs
  
  NullPointerException - if os == null
- write
  
  public void write(int b) throws IOException
  
  Specified by:
  
  write in class OutputStream
  
  Throws:
  
  IOException
- write
  
  public void write(byte[] ba) throws IOException
  
  Overrides:
  
  write in class OutputStream
  
  Throws:
  
  IOException
- write
  
  public void write(byte[] buf, int off, int len) throws IOException
  
  Overrides:
  
  write in class OutputStream
  
  Throws:
  
  IOException
- flush
  
  public void flush() throws IOException
  
  Specified by:
  
  flush in interface Flushable
  
  Overrides:
  
  flush in class OutputStream
  
  Throws:
  
  IOException
- close
  
  public void close() throws IOException
  
  Specified by:
  
  close in interface AutoCloseable
  
  Specified by:
  
  close in interface Closeable
  
  Overrides:
  
  close in class OutputStream
  
  Throws:
  
  IOException

Class BGZIPOutputStream

Constructor Summary

Method Summary

Methods inherited from class java.io.OutputStream

Methods inherited from class java.lang.Object

Constructor Details

BGZIPOutputStream

Method Details

main

writeEmptyBlock

write

write

write

flush

close