htsjdk.samtools.cram.encoding.readfeatures

Class Substitution

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.Substitution

All Implemented Interfaces:

ReadFeature, java.io.Serializable

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

A substitution event captured in read coordinates. It is characterized by position in read, read base and reference base. The class is also responsible for converting combinations of read base and reference base into a byte value (code).

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_CODE
static byte	operator

Constructor Summary

Constructors

Constructor and Description
Substitution()

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

NO_CODE

public static final int NO_CODE

See Also:

Constant Field Values

operator

public static final byte operator

See Also:

Constant Field Values

Constructor Detail

Substitution

public Substitution()

Method Detail

getCode

public byte getCode()

setCode

public void setCode(byte code)

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

getBase

public byte getBase()

setBase

public void setBase(byte base)

getReferenceBase

public byte getReferenceBase()

setReferenceBase

public void setReferenceBase(byte referenceBase)

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