org.seqdoop.hadoop_bam.util

Class BGZFBlockIndex

java.lang.Object

org.seqdoop.hadoop_bam.util.BGZFBlockIndex

public final class BGZFBlockIndex
extends Object

An index into BGZF-compressed files, for BGZFSplitFileInputFormat. Reads files that are created by BGZFBlockIndexer.

Indexes the positions of individual gzip blocks in the file.

Constructor Summary

Constructors

Constructor and Description
BGZFBlockIndex()
BGZFBlockIndex(File path)
BGZFBlockIndex(InputStream in)

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args) Writes some statistics about each BGZF block index file given as an argument.
Long	nextBlock(long filePos)
Long	prevBlock(long filePos)
void	readIndex(InputStream in)
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

BGZFBlockIndex

public BGZFBlockIndex()

BGZFBlockIndex

public BGZFBlockIndex(File path)
               throws IOException

Throws:

IOException

BGZFBlockIndex

public BGZFBlockIndex(InputStream in)
               throws IOException

Throws:

IOException

Method Detail

readIndex

public void readIndex(InputStream in)
               throws IOException

Throws:

IOException

prevBlock

public Long prevBlock(long filePos)

nextBlock

public Long nextBlock(long filePos)

size

public int size()

main

public static void main(String[] args)

Writes some statistics about each BGZF block index file given as an argument.