CigarOperator (htsjdk 2.8.1 API)

java.lang.Object
- java.lang.Enum<CigarOperator>
- - htsjdk.samtools.CigarOperator

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<CigarOperator>
```
public enum CigarOperator
extends java.lang.Enum<CigarOperator>
```
The operators that can appear in a cigar string, and information about their disk representations.

Enum Constant Summary

Enum Constants
Enum Constant and Description
`D` Deletion vs.
`EQ` Matches the reference.
`H` Hard clip.
`I` Insertion vs.
`M` Match or mismatch
`N` Skipped region from the reference.
`P` Padding.
`S` Soft clip.
`X` Mismatches the reference.

Field Summary

Fields
Modifier and Type	Field and Description
`static CigarOperator`	`DELETION`
`static CigarOperator`	`HARD_CLIP`
`static CigarOperator`	`INSERTION`
`static CigarOperator`	`MATCH_OR_MISMATCH`
`static CigarOperator`	`PADDING`
`static CigarOperator`	`SKIPPED_REGION`
`static CigarOperator`	`SOFT_CLIP`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static CigarOperator`	`binaryToEnum(int i)`
`static CigarOperator`	`characterToEnum(int b)`
`boolean`	`consumesReadBases()` If true, represents that this cigar operator "consumes" bases from the read bases.
`boolean`	`consumesReferenceBases()` If true, represents that this cigar operator "consumes" bases from the reference sequence.
`static int`	`enumToBinary(CigarOperator e)`
`static byte`	`enumToCharacter(CigarOperator e)` Returns the character that should be used within a SAM file.
`boolean`	`isAlignment()` Returns true if the operator is a M, a X or a EQ
`boolean`	`isClipping()` Returns true if the operator is a clipped (hard or soft) operator
`boolean`	`isIndel()` Returns true if the operator is a Insertion or Deletion operator
`boolean`	`isIndelOrSkippedRegion()` Returns true if the operator is a Skipped Region Insertion or Deletion operator
`boolean`	`isPadding()` Returns true if the operator is a Padding operator
`java.lang.String`	`toString()` Returns the cigar operator as it would be seen in a SAM file.
`static CigarOperator`	`valueOf(java.lang.String name)` Returns the enum constant of this type with the specified name.
`static CigarOperator[]`	`values()` Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Enum Constant Detail
  - M
```
public static final CigarOperator M
```
    Match or mismatch
  - I
```
public static final CigarOperator I
```
    Insertion vs. the reference.
  - D
```
public static final CigarOperator D
```
    Deletion vs. the reference.
  - N
```
public static final CigarOperator N
```
    Skipped region from the reference.
  - S
```
public static final CigarOperator S
```
    Soft clip.
  - H
```
public static final CigarOperator H
```
    Hard clip.
  - P
```
public static final CigarOperator P
```
    Padding.
  - EQ
```
public static final CigarOperator EQ
```
    Matches the reference.
  - X
```
public static final CigarOperator X
```
    Mismatches the reference.
- Field Detail
  - MATCH_OR_MISMATCH
```
public static final CigarOperator MATCH_OR_MISMATCH
```
  - INSERTION
```
public static final CigarOperator INSERTION
```
  - DELETION
```
public static final CigarOperator DELETION
```
  - SKIPPED_REGION
```
public static final CigarOperator SKIPPED_REGION
```
  - SOFT_CLIP
```
public static final CigarOperator SOFT_CLIP
```
  - HARD_CLIP
```
public static final CigarOperator HARD_CLIP
```
  - PADDING
```
public static final CigarOperator PADDING
```
- Method Detail
  - values
```
public static CigarOperator[] values()
```
    Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
```
for (CigarOperator c : CigarOperator.values())
    System.out.println(c);
```
    Returns:
    
    an array containing the constants of this enum type, in the order they are declared
  - valueOf
```
public static CigarOperator valueOf(java.lang.String name)
```
    Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
    
    Parameters:
    
    name - the name of the enum constant to be returned.
    
    Returns:
    
    the enum constant with the specified name
    
    Throws:
    
    java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
    
    java.lang.NullPointerException - if the argument is null
  - consumesReadBases
```
public boolean consumesReadBases()
```
    If true, represents that this cigar operator "consumes" bases from the read bases.
  - consumesReferenceBases
```
public boolean consumesReferenceBases()
```
    If true, represents that this cigar operator "consumes" bases from the reference sequence.
  - characterToEnum
```
public static CigarOperator characterToEnum(int b)
```
    Parameters:
    
    b - CIGAR operator in character form as appears in a text CIGAR string
    
    Returns:
    
    CigarOperator enum value corresponding to the given character.
  - binaryToEnum
```
public static CigarOperator binaryToEnum(int i)
```
    Parameters:
    
    i - CIGAR operator in binary form as appears in a BAMRecord.
    
    Returns:
    
    CigarOperator enum value corresponding to the given int value.
  - enumToBinary
```
public static int enumToBinary(CigarOperator e)
```
    Parameters:
    
    e - CigarOperator enum value.
    
    Returns:
    
    CIGAR operator corresponding to the enum value in binary form as appears in a BAMRecord.
  - enumToCharacter
```
public static byte enumToCharacter(CigarOperator e)
```
    Returns the character that should be used within a SAM file.
  - isClipping
```
public boolean isClipping()
```
    Returns true if the operator is a clipped (hard or soft) operator
  - isIndel
```
public boolean isIndel()
```
    Returns true if the operator is a Insertion or Deletion operator
  - isIndelOrSkippedRegion
```
public boolean isIndelOrSkippedRegion()
```
    Returns true if the operator is a Skipped Region Insertion or Deletion operator
  - isAlignment
```
public boolean isAlignment()
```
    Returns true if the operator is a M, a X or a EQ
  - isPadding
```
public boolean isPadding()
```
    Returns true if the operator is a Padding operator
  - toString
```
public java.lang.String toString()
```
    Returns the cigar operator as it would be seen in a SAM file.
    
    Overrides:
    
    toString in class java.lang.Enum<CigarOperator>

Enum CigarOperator

Enum Constant Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

M

I

D

N

S

H

P

EQ

X

Field Detail

MATCH_OR_MISMATCH

INSERTION

DELETION

SKIPPED_REGION

SOFT_CLIP

HARD_CLIP

PADDING

Method Detail

values

valueOf

consumesReadBases

consumesReferenceBases

characterToEnum

binaryToEnum

enumToBinary

enumToCharacter

isClipping

isIndel

isIndelOrSkippedRegion

isAlignment

isPadding

toString