Package htsjdk.samtools

Enum Class SAMTag

java.lang.Object

java.lang.Enum<SAMTag>

htsjdk.samtools.SAMTag

All Implemented Interfaces:

Serializable, Comparable<SAMTag>, Constable

public enum SAMTag
extends Enum<SAMTag>

The standard tags for a SAM record that are defined in the SAM spec.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
AM
AS
BC
BQ
BZ
CB
CC
CG
CM
CO
CP
CQ
CR
CS
CT
CY
E2
FI
FS
FT
FZ
GC	Deprecated. for backwards compatibility only
GQ	Deprecated. for backwards compatibility only
GS	Deprecated. for backwards compatibility only
H0
H1
H2
HI
IH
LB
MC
MD
MF	Deprecated. for backwards compatibility only
MI
MQ
NH
NM
OA
OC
OF
OP
OQ
OR
OX
PG
PQ
PT
PU
Q2
QT
QX
R2
RG
RT	Deprecated. use BC instead, for backwards compatibilty only
RX
S2	Deprecated. for backwards compatibility only
SA
SM
SQ	Deprecated. for backwards compatibility only
TC
U2
UQ

Method Summary

Modifier and Type	Method	Description
short	getBinaryTag()	Get the binary representation of this tag name.
static short	makeBinaryTag(String tag)	Convert from String representation of tag name to short representation.
static String	makeStringTag(short tag)	Convert from short representation of tag name to String representation.
static SAMTag	valueOf(String name)	Returns the enum constant of this class with the specified name.
static SAMTag[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

AM

public static final SAMTag AM

AS

public static final SAMTag AS

BC

public static final SAMTag BC

BQ

public static final SAMTag BQ

BZ

public static final SAMTag BZ

CB

public static final SAMTag CB

CC

public static final SAMTag CC

CG

public static final SAMTag CG

CM

public static final SAMTag CM

CO

public static final SAMTag CO

CP

public static final SAMTag CP

CQ

public static final SAMTag CQ

CR

public static final SAMTag CR

CS

public static final SAMTag CS

CT

public static final SAMTag CT

CY

public static final SAMTag CY

E2

public static final SAMTag E2

FI

public static final SAMTag FI

FS

public static final SAMTag FS

FT

public static final SAMTag FT

FZ

public static final SAMTag FZ

GC

@Deprecated
public static final SAMTag GC

Deprecated.

for backwards compatibility only

GS

@Deprecated
public static final SAMTag GS

Deprecated.

for backwards compatibility only

GQ

@Deprecated
public static final SAMTag GQ

Deprecated.

for backwards compatibility only

LB

public static final SAMTag LB

H0

public static final SAMTag H0

H1

public static final SAMTag H1

H2

public static final SAMTag H2

HI

public static final SAMTag HI

IH

public static final SAMTag IH

MC

public static final SAMTag MC

MF

@Deprecated
public static final SAMTag MF

Deprecated.

for backwards compatibility only

MI

public static final SAMTag MI

MD

public static final SAMTag MD

MQ

public static final SAMTag MQ

NH

public static final SAMTag NH

NM

public static final SAMTag NM

OA

public static final SAMTag OA

OQ

public static final SAMTag OQ

OP

public static final SAMTag OP

OC

public static final SAMTag OC

OF

public static final SAMTag OF

OR

public static final SAMTag OR

OX

public static final SAMTag OX

PG

public static final SAMTag PG

PQ

public static final SAMTag PQ

PT

public static final SAMTag PT

PU

public static final SAMTag PU

Q2

public static final SAMTag Q2

QT

public static final SAMTag QT

QX

public static final SAMTag QX

R2

public static final SAMTag R2

RG

public static final SAMTag RG

RT

@Deprecated
public static final SAMTag RT

Deprecated.

use BC instead, for backwards compatibilty only

RX

public static final SAMTag RX

S2

@Deprecated
public static final SAMTag S2

Deprecated.

for backwards compatibility only

SA

public static final SAMTag SA

SM

public static final SAMTag SM

SQ

@Deprecated
public static final SAMTag SQ

Deprecated.

for backwards compatibility only

TC

public static final SAMTag TC

U2

public static final SAMTag U2

UQ

public static final SAMTag UQ

Method Details

values

public static SAMTag[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static SAMTag valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null

makeBinaryTag

public static short makeBinaryTag(String tag)

Convert from String representation of tag name to short representation.

Parameters:

tag - 2-character String representation of a tag name.

Returns:

Tag name packed as 2 ASCII bytes in a short.

makeStringTag

public static String makeStringTag(short tag)

Convert from short representation of tag name to String representation.

Parameters:

tag - Tag name packed as 2 ASCII bytes in a short.

Returns:

2-character String representation of a tag name.

getBinaryTag

public short getBinaryTag()

Get the binary representation of this tag name.

Returns:

the binary representation of this tag name

See Also:

• makeBinaryTag(String)