htsjdk.samtools.cram.encoding.readfeatures

Class Scores

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.Scores

All Implemented Interfaces:

ReadFeature, java.io.Serializable

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

A read feature representing a contiguous stretch of quality scores in a read.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static byte	operator

Constructor Summary

Constructors

Constructor and Description
Scores()
Scores(int position, byte[] sequence)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
byte	getOperator() Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
byte[]	getScores()
void	setPosition(int position)
void	setScores(byte[] scores)
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

Scores

public Scores()

Scores

public Scores(int position,
              byte[] sequence)

Method Detail

getScores

public byte[] getScores()

setScores

public void setScores(byte[] scores)

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

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