Package htsjdk.samtools.cram.encoding.readfeatures

Class SoftClip

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.SoftClip

All Implemented Interfaces:

ReadFeature, Serializable

public class SoftClip
extends Object
implements Serializable, ReadFeature

A read feature representing a soft clip similar to CigarOperator.S.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final byte	operator

Constructor Summary

Constructors

Constructor	Description
SoftClip(int position, byte[] sequence)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
byte	getOperator()	Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
byte[]	getSequence()
int	hashCode()
void	setSequence(byte[] sequence)
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

SoftClip

public SoftClip(int position,
 byte[] sequence)

Method Details

getSequence

public byte[] getSequence()

setSequence

public void setSequence(byte[] sequence)

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

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object