Package htsjdk.samtools.cram.encoding.readfeatures

Class Substitution

java.lang.Object

htsjdk.samtools.cram.encoding.readfeatures.Substitution

All Implemented Interfaces:

ReadFeature, Serializable

public class Substitution
extends Object
implements 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). Both reference and read bases must be ACGTN only.

See Also:

• Serialized Form

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
Substitution(int position, byte code)
Substitution(int position, byte base, byte referenceBase)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
byte	getBase()
byte	getCode()
byte	getOperator()	Read features are distinguished by operator, similar to cigar operator.
int	getPosition()
byte	getReferenceBase()
int	hashCode()
void	setCode(byte code)
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

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 Details

Substitution

public Substitution(int position,
 byte code)

Substitution

public Substitution(int position,
 byte base,
 byte referenceBase)

Method Details

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

getBase

public byte getBase()

getReferenceBase

public byte getReferenceBase()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object