Package htsjdk.samtools
Enum SAMTag
- java.lang.Object
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- java.lang.Enum<SAMTag>
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- htsjdk.samtools.SAMTag
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- All Implemented Interfaces:
Serializable
,Comparable<SAMTag>
public enum SAMTag extends Enum<SAMTag>
The standard tags for a SAM record that are defined in the SAM spec.
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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 onlyGQ
Deprecated.for backwards compatibility onlyGS
Deprecated.for backwards compatibility onlyH0
H1
H2
HI
IH
LB
MC
MD
MF
Deprecated.for backwards compatibility onlyMI
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 onlyRX
S2
Deprecated.for backwards compatibility onlySA
SM
SQ
Deprecated.for backwards compatibility onlyTC
U2
UQ
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 type with the specified name.static SAMTag[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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AM
public static final SAMTag AM
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AS
public static final SAMTag AS
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BC
public static final SAMTag BC
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BQ
public static final SAMTag BQ
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BZ
public static final SAMTag BZ
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CB
public static final SAMTag CB
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CC
public static final SAMTag CC
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CG
public static final SAMTag CG
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CM
public static final SAMTag CM
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CO
public static final SAMTag CO
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CP
public static final SAMTag CP
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CQ
public static final SAMTag CQ
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CR
public static final SAMTag CR
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CS
public static final SAMTag CS
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CT
public static final SAMTag CT
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CY
public static final SAMTag CY
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E2
public static final SAMTag E2
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FI
public static final SAMTag FI
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FS
public static final SAMTag FS
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FT
public static final SAMTag FT
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FZ
public static final SAMTag FZ
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GC
@Deprecated public static final SAMTag GC
Deprecated.for backwards compatibility only
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GS
@Deprecated public static final SAMTag GS
Deprecated.for backwards compatibility only
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GQ
@Deprecated public static final SAMTag GQ
Deprecated.for backwards compatibility only
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LB
public static final SAMTag LB
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H0
public static final SAMTag H0
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H1
public static final SAMTag H1
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H2
public static final SAMTag H2
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HI
public static final SAMTag HI
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IH
public static final SAMTag IH
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MC
public static final SAMTag MC
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MF
@Deprecated public static final SAMTag MF
Deprecated.for backwards compatibility only
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MI
public static final SAMTag MI
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MD
public static final SAMTag MD
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MQ
public static final SAMTag MQ
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NH
public static final SAMTag NH
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NM
public static final SAMTag NM
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OA
public static final SAMTag OA
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OQ
public static final SAMTag OQ
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OP
public static final SAMTag OP
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OC
public static final SAMTag OC
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OF
public static final SAMTag OF
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OR
public static final SAMTag OR
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OX
public static final SAMTag OX
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PG
public static final SAMTag PG
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PQ
public static final SAMTag PQ
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PT
public static final SAMTag PT
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PU
public static final SAMTag PU
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Q2
public static final SAMTag Q2
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QT
public static final SAMTag QT
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QX
public static final SAMTag QX
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R2
public static final SAMTag R2
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RG
public static final SAMTag RG
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RT
@Deprecated public static final SAMTag RT
Deprecated.use BC instead, for backwards compatibilty only
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RX
public static final SAMTag RX
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S2
@Deprecated public static final SAMTag S2
Deprecated.for backwards compatibility only
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SA
public static final SAMTag SA
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SM
public static final SAMTag SM
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SQ
@Deprecated public static final SAMTag SQ
Deprecated.for backwards compatibility only
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TC
public static final SAMTag TC
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U2
public static final SAMTag U2
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UQ
public static final SAMTag UQ
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Method Detail
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values
public static SAMTag[] 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 (SAMTag c : SAMTag.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static SAMTag valueOf(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:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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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.
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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.
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getBinaryTag
public short getBinaryTag()
Get the binary representation of this tag name.- Returns:
- the binary representation of this tag name
- See Also:
makeBinaryTag(String)
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