htsjdk.samtools

Enum CigarOperator

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

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.
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.

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>