org.seqdoop.hadoop_bam

Class SplittingBAMIndex

java.lang.Object

org.seqdoop.hadoop_bam.SplittingBAMIndex

public final class SplittingBAMIndex
extends Object

An index into BAM files, for BAMInputFormat. Reads files that are created by SplittingBAMIndexer.

Indexes the positions of individual BAM records in the file.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
List<Long>	getVirtualOffsets()
int	hashCode()
static void	main(String[] args) Writes some statistics about each splitting BAM index file given as an argument.
Long	nextAlignment(long filePos)
Long	prevAlignment(long filePos)
void	readIndex(InputStream in)
int	size()
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SplittingBAMIndex

public SplittingBAMIndex()

SplittingBAMIndex

public SplittingBAMIndex(File path)
                  throws IOException

Throws:

IOException

SplittingBAMIndex

public SplittingBAMIndex(InputStream in)
                  throws IOException

Throws:

IOException

Method Detail

readIndex

public void readIndex(InputStream in)
               throws IOException

Throws:

IOException

getVirtualOffsets

public List<Long> getVirtualOffsets()

prevAlignment

public Long prevAlignment(long filePos)

nextAlignment

public Long nextAlignment(long filePos)

size

public int size()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

main

public static void main(String[] args)

Writes some statistics about each splitting BAM index file given as an argument.