htsjdk.samtools.cram.encoding.core

Class BetaIntegerCodec

java.lang.Object

htsjdk.samtools.cram.encoding.core.CoreCodec<java.lang.Integer>

htsjdk.samtools.cram.encoding.core.BetaIntegerCodec

All Implemented Interfaces:

CRAMCodec<java.lang.Integer>

public class BetaIntegerCodec
extends CoreCodec<java.lang.Integer>

Encodes integers by adding a constant offset value to a range of values in order to reduce the necessary number of bits needed to store each value. As a simple example, consider a data series with values all in the range 10,000 - 10,100. Choosing the offset -10,000 means every encoded value will be stored as 0 - 100, requiring only ceil(log2(100)) = 7 bits per value.

Field Summary

Fields inherited from class htsjdk.samtools.cram.encoding.core.CoreCodec

coreBlockInputStream, coreBlockOutputStream

Constructor Summary

Constructors

Constructor and Description
BetaIntegerCodec(BitInputStream coreBlockInputStream, BitOutputStream coreBlockOutputStream, int offset, int bitsPerValue) Given integers to encode in the range MIN to MAX:

Method Summary

Modifier and Type	Method and Description
java.lang.Integer	read() Read a single object from the stream
java.lang.Integer	read(int length) Read a array of specified length from the stream
void	write(java.lang.Integer value) Write an object to the stream

Methods inherited from class java.lang.Object

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

Constructor Detail

BetaIntegerCodec

public BetaIntegerCodec(BitInputStream coreBlockInputStream,
                        BitOutputStream coreBlockOutputStream,
                        int offset,
                        int bitsPerValue)

Given integers to encode in the range MIN to MAX:

Parameters:

offset - the common value to be added to all values before storage. Setting this to (-MIN) will ensure all stored values will be in the range (0 .. MAX - MIN)

bitsPerValue - the smallest value which will allow the largest stored value (MAX - MIN)

Method Detail

read

public final java.lang.Integer read()

Description copied from interface: CRAMCodec

Read a single object from the stream

Returns:

an object from the stream

read

public java.lang.Integer read(int length)

Description copied from interface: CRAMCodec

Read a array of specified length from the stream

Parameters:

length - the number of elements to read

Returns:

an object from the stream

write

public final void write(java.lang.Integer value)

Description copied from interface: CRAMCodec

Write an object to the stream

Parameters:

value - the object to write