htsjdk.samtools.cram.encoding.readfeatures

Class HardClip

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.HardClip

All Implemented Interfaces:

ReadFeature, java.io.Serializable

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

A read feature representing a hard clip similar to CigarOperator.H.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static byte	operator

Constructor Summary

Constructors

Constructor and Description
HardClip()
HardClip(int position, int length)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
int	getLength()
byte	getOperator() Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
void	setLength(int length)
void	setPosition(int position)
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

HardClip

public HardClip()

HardClip

public HardClip(int position,
                int length)

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

getLength

public int getLength()

setLength

public void setLength(int length)

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