SAMTagUtil (htsjdk 2.20.3 API)

java.lang.Object
- htsjdk.samtools.SAMTagUtil

Deprecated.
as of 11/2018, the functions in this class have been absorbed by the SAMTag enum.
```
@Deprecated
public class SAMTagUtil
extends java.lang.Object
```
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 and Description
`short`	`AM` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`AS` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`BC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`BQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`BZ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CB` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CG` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CM` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CO` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CP` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CR` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CS` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CT` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`CY` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`E2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`FI` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`FS` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`FT` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`FZ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`GC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`GQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`GS` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`H0` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`H1` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`H2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`HI` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`IH` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`LB` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`MC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`MD` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`MF` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`MI` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`MQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`NH` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`NM` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OF` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OP` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OR` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`OX` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`PG` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`PQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`PT` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`PU` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`Q2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`QT` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`QX` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`R2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`RG` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`RT` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`RX` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`S2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`SA` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`SM` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`SQ` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`TC` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`U2` Deprecated. use `SAMTag.getBinaryTag()` instead.
`short`	`UQ` Deprecated. use `SAMTag.getBinaryTag()` instead.

Constructor Summary

Constructors
Constructor and Description

SAMTagUtil()
Deprecated.

Constructors
Constructor and Description
`SAMTagUtil()` Deprecated.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static SAMTagUtil`	`getSingleton()` Deprecated. use the static methods in `SAMTag` instead
`short`	`makeBinaryTag(java.lang.String tag)` Deprecated. use `instead`
`java.lang.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 Detail
  - 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 Detail
  - SAMTagUtil
```
public SAMTagUtil()
```
    Deprecated.
- Method Detail
  - 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(java.lang.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 java.lang.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 Detail

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 Detail

SAMTagUtil

Method Detail

getSingleton

makeBinaryTag

makeStringTag