htsjdk.samtools.SAMTagUtil

@Deprecated public class SAMTagUtil extends Object

Deprecated.

as of 11/2018, the functions in this class have been absorbed by the SAMTag enum.

Facility for converting between String and short representation of a SAM tag. short representation is used by HTSJDK internally and is much more efficient. Callers are encouraged to obtain the short value for a tag of interest once, and then use the SAMRecord attribute API that takes shorts rather than Strings. Tags that are defined by the SAM spec are included in the enum SAMTag along with their precomputed short tag.

Field Summary

Fields

Modifier and Type

Field

Description

final short

AM

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

AS

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

BC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

BQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

BZ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CB

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CG

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CM

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CO

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CP

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CR

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CS

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CT

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

CY

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

E2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

FI

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

FS

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

FT

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

FZ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

GC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

GQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

GS

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

H0

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

H1

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

H2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

HI

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

IH

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

LB

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

MC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

MD

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

MF

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

MI

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

MQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

NH

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

NM

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OF

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OP

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OR

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

OX

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

PG

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

PQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

PT

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

PU

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

Q2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

QT

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

QX

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

R2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

RG

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

RT

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

RX

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

S2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

SA

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

SM

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

SQ

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

TC

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

U2

Deprecated.
use SAMTag.getBinaryTag() instead.

final short

UQ

Deprecated.
use SAMTag.getBinaryTag() instead.
Constructor Summary

Constructors

Constructor

Description

SAMTagUtil()

Deprecated.
Method Summary

Modifier and Type

Method

Description

static SAMTagUtil

getSingleton()

Deprecated.
use the static methods in SAMTag instead

short

makeBinaryTag(String tag)

Deprecated.
use instead

String

makeStringTag(short tag)

Deprecated.
use SAMTag.makeStringTag(short) instead

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- AM
  
  @Deprecated public final short AM
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- AS
  
  @Deprecated public final short AS
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- BC
  
  @Deprecated public final short BC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- BQ
  
  @Deprecated public final short BQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- BZ
  
  @Deprecated public final short BZ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CB
  
  @Deprecated public final short CB
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CC
  
  @Deprecated public final short CC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CG
  
  @Deprecated public final short CG
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CM
  
  @Deprecated public final short CM
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CO
  
  @Deprecated public final short CO
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CP
  
  @Deprecated public final short CP
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CQ
  
  @Deprecated public final short CQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CR
  
  @Deprecated public final short CR
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CS
  
  @Deprecated public final short CS
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CT
  
  @Deprecated public final short CT
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- CY
  
  @Deprecated public final short CY
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- E2
  
  @Deprecated public final short E2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- FI
  
  @Deprecated public final short FI
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- FS
  
  @Deprecated public final short FS
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- FT
  
  @Deprecated public final short FT
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- FZ
  
  @Deprecated public final short FZ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- GC
  
  @Deprecated public final short GC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- GS
  
  @Deprecated public final short GS
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- GQ
  
  @Deprecated public final short GQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- LB
  
  @Deprecated public final short LB
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- H0
  
  @Deprecated public final short H0
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- H1
  
  @Deprecated public final short H1
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- H2
  
  @Deprecated public final short H2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- HI
  
  @Deprecated public final short HI
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- IH
  
  @Deprecated public final short IH
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- MC
  
  @Deprecated public final short MC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- MF
  
  @Deprecated public final short MF
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- MI
  
  @Deprecated public final short MI
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- MD
  
  @Deprecated public final short MD
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- MQ
  
  @Deprecated public final short MQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- NH
  
  @Deprecated public final short NH
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- NM
  
  @Deprecated public final short NM
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OQ
  
  @Deprecated public final short OQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OP
  
  @Deprecated public final short OP
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OC
  
  @Deprecated public final short OC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OF
  
  @Deprecated public final short OF
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OR
  
  @Deprecated public final short OR
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- OX
  
  @Deprecated public final short OX
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- PG
  
  @Deprecated public final short PG
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- PQ
  
  @Deprecated public final short PQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- PT
  
  @Deprecated public final short PT
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- PU
  
  @Deprecated public final short PU
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- QT
  
  @Deprecated public final short QT
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- Q2
  
  @Deprecated public final short Q2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- QX
  
  @Deprecated public final short QX
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- R2
  
  @Deprecated public final short R2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- RG
  
  @Deprecated public final short RG
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- RT
  
  @Deprecated public final short RT
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- RX
  
  @Deprecated public final short RX
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- S2
  
  @Deprecated public final short S2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- SA
  
  @Deprecated public final short SA
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- SM
  
  @Deprecated public final short SM
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- SQ
  
  @Deprecated public final short SQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- TC
  
  @Deprecated public final short TC
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- U2
  
  @Deprecated public final short U2
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
- UQ
  
  @Deprecated public final short UQ
  
  Deprecated.
  use SAMTag.getBinaryTag() instead.
Constructor Details
- SAMTagUtil
  
  public SAMTagUtil()
  
  Deprecated.
Method Details
- getSingleton
  
  @Deprecated public static SAMTagUtil getSingleton()
  
  Deprecated.
  use the static methods in SAMTag instead
  
  Despite the fact that this class has state, it should be thread-safe because the cache gets filled with the same values by any thread.
- makeBinaryTag
  
  @Deprecated public short makeBinaryTag(String tag)
  
  Deprecated.
  use instead
  
  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
  
  @Deprecated public String makeStringTag(short tag)
  
  Deprecated.
  use SAMTag.makeStringTag(short) instead
  
  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.

Class SAMTagUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

AM

AS

BC

BQ

BZ

CB

CC

CG

CM

CO

CP

CQ

CR

CS

CT

CY

E2

FI

FS

FT

FZ

GC

GS

GQ

LB

H0

H1

H2

HI

IH

MC

MF

MI

MD

MQ

NH

NM

OQ

OP

OC

OF

OR

OX

PG

PQ

PT

PU

QT

Q2

QX

R2

RG

RT

RX

S2

SA

SM

SQ

TC

U2

UQ

Constructor Details

SAMTagUtil

Method Details

getSingleton

makeBinaryTag

makeStringTag