htsjdk.samtools.cram.encoding.readfeatures

Class SoftClip

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.SoftClip

All Implemented Interfaces:

ReadFeature, java.io.Serializable

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

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

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static byte	operator

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

operator

public static final byte operator

See Also:

Constant Field Values

Constructor Detail

SoftClip

public SoftClip()

SoftClip

public SoftClip(int position,
                byte[] sequence)

Method Detail

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

setPosition

public void setPosition(int position)

Specified by:

setPosition in interface ReadFeature

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object