htsjdk.samtools.cram.encoding.readfeatures

Class ReadBase

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.ReadBase

All Implemented Interfaces:

ReadFeature, java.io.Serializable

public class ReadBase
extends java.lang.Object
implements java.io.Serializable, ReadFeature

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

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static byte	operator

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
byte	getBase()
byte	getOperator() Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
byte	getQualityScore()
void	setBase(byte base)
void	setPosition(int position)
void	setQualityScore(byte qualityScore)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

operator

public static final byte operator

See Also:

Constant Field Values

Constructor Detail

ReadBase

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

Method Detail

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

setPosition

public void setPosition(int position)

Specified by:

setPosition in interface ReadFeature

getQualityScore

public byte getQualityScore()

setQualityScore

public void setQualityScore(byte qualityScore)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getBase

public byte getBase()

setBase

public void setBase(byte base)