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 int NO_CODE

static byte operator

Constructor Summary

Constructors
Constructor Description

Substitution()

Substitution(int position, byte base, byte referenceBase)

Method Summary

All Methods Instance Methods Concrete Methods
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()`
`void`	`setBase(byte base)`
`void`	`setCode(byte code)`
`void`	`setPosition(int position)`
`void`	`setReferenceBase(byte referenceBase)`
`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()
```
  - Substitution
```
public Substitution(int position,
                    byte base,
                    byte referenceBase)
```
- 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(Object obj)
```
    Overrides:
    
    equals in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

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

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

Class Substitution

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NO_CODE

operator

Constructor Detail

Substitution

Substitution

Method Detail

getCode

setCode

getOperator

getPosition

setPosition

getBase

setBase

getReferenceBase

setReferenceBase

equals

toString