Package htsjdk.samtools.cram.encoding.readfeatures

Class ReadBase

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.ReadBase

All Implemented Interfaces:

ReadFeature, Serializable

public class ReadBase
extends Object
implements Serializable, ReadFeature

A read feature representing a single base with associated quality score.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final byte	operator

Constructor Summary

Constructors

Constructor	Description
ReadBase(int position, byte base, byte qualityScore)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
byte	getBase()
byte	getOperator()	Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
byte	getQualityScore()
int	hashCode()
void	setBase(byte base)
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

operator

public static final byte operator

See Also:

• Constant Field Values

Constructor Details

ReadBase

public ReadBase(int position,
 byte base,
 byte qualityScore)

Method Details

getOperator

public byte getOperator()

Description copied from interface: ReadFeature

Read features are distinguished by operator, similar to cigar operator.

Specified by:

getOperator in interface ReadFeature

Returns:

type of the read feature

getPosition

public int getPosition()

Specified by:

getPosition in interface ReadFeature

Returns:

zero-based position in the read

getQualityScore

public byte getQualityScore()

toString

public String toString()

Overrides:

toString in class Object

getBase

public byte getBase()

setBase

public void setBase(byte base)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object