Package htsjdk.samtools
Class SAMTagUtil
- java.lang.Object
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- htsjdk.samtools.SAMTagUtil
-
@Deprecated public class SAMTagUtil extends Object
Deprecated.as of 11/2018, the functions in this class have been absorbed by theSAMTag
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 enumSAMTag
along with their precomputed short tag.
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-
Field Summary
Fields Modifier and Type Field Description short
AM
Deprecated.useSAMTag.getBinaryTag()
instead.short
AS
Deprecated.useSAMTag.getBinaryTag()
instead.short
BC
Deprecated.useSAMTag.getBinaryTag()
instead.short
BQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
BZ
Deprecated.useSAMTag.getBinaryTag()
instead.short
CB
Deprecated.useSAMTag.getBinaryTag()
instead.short
CC
Deprecated.useSAMTag.getBinaryTag()
instead.short
CG
Deprecated.useSAMTag.getBinaryTag()
instead.short
CM
Deprecated.useSAMTag.getBinaryTag()
instead.short
CO
Deprecated.useSAMTag.getBinaryTag()
instead.short
CP
Deprecated.useSAMTag.getBinaryTag()
instead.short
CQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
CR
Deprecated.useSAMTag.getBinaryTag()
instead.short
CS
Deprecated.useSAMTag.getBinaryTag()
instead.short
CT
Deprecated.useSAMTag.getBinaryTag()
instead.short
CY
Deprecated.useSAMTag.getBinaryTag()
instead.short
E2
Deprecated.useSAMTag.getBinaryTag()
instead.short
FI
Deprecated.useSAMTag.getBinaryTag()
instead.short
FS
Deprecated.useSAMTag.getBinaryTag()
instead.short
FT
Deprecated.useSAMTag.getBinaryTag()
instead.short
FZ
Deprecated.useSAMTag.getBinaryTag()
instead.short
GC
Deprecated.useSAMTag.getBinaryTag()
instead.short
GQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
GS
Deprecated.useSAMTag.getBinaryTag()
instead.short
H0
Deprecated.useSAMTag.getBinaryTag()
instead.short
H1
Deprecated.useSAMTag.getBinaryTag()
instead.short
H2
Deprecated.useSAMTag.getBinaryTag()
instead.short
HI
Deprecated.useSAMTag.getBinaryTag()
instead.short
IH
Deprecated.useSAMTag.getBinaryTag()
instead.short
LB
Deprecated.useSAMTag.getBinaryTag()
instead.short
MC
Deprecated.useSAMTag.getBinaryTag()
instead.short
MD
Deprecated.useSAMTag.getBinaryTag()
instead.short
MF
Deprecated.useSAMTag.getBinaryTag()
instead.short
MI
Deprecated.useSAMTag.getBinaryTag()
instead.short
MQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
NH
Deprecated.useSAMTag.getBinaryTag()
instead.short
NM
Deprecated.useSAMTag.getBinaryTag()
instead.short
OC
Deprecated.useSAMTag.getBinaryTag()
instead.short
OF
Deprecated.useSAMTag.getBinaryTag()
instead.short
OP
Deprecated.useSAMTag.getBinaryTag()
instead.short
OQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
OR
Deprecated.useSAMTag.getBinaryTag()
instead.short
OX
Deprecated.useSAMTag.getBinaryTag()
instead.short
PG
Deprecated.useSAMTag.getBinaryTag()
instead.short
PQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
PT
Deprecated.useSAMTag.getBinaryTag()
instead.short
PU
Deprecated.useSAMTag.getBinaryTag()
instead.short
Q2
Deprecated.useSAMTag.getBinaryTag()
instead.short
QT
Deprecated.useSAMTag.getBinaryTag()
instead.short
QX
Deprecated.useSAMTag.getBinaryTag()
instead.short
R2
Deprecated.useSAMTag.getBinaryTag()
instead.short
RG
Deprecated.useSAMTag.getBinaryTag()
instead.short
RT
Deprecated.useSAMTag.getBinaryTag()
instead.short
RX
Deprecated.useSAMTag.getBinaryTag()
instead.short
S2
Deprecated.useSAMTag.getBinaryTag()
instead.short
SA
Deprecated.useSAMTag.getBinaryTag()
instead.short
SM
Deprecated.useSAMTag.getBinaryTag()
instead.short
SQ
Deprecated.useSAMTag.getBinaryTag()
instead.short
TC
Deprecated.useSAMTag.getBinaryTag()
instead.short
U2
Deprecated.useSAMTag.getBinaryTag()
instead.short
UQ
Deprecated.useSAMTag.getBinaryTag()
instead.
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Constructor Summary
Constructors Constructor Description SAMTagUtil()
Deprecated.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static SAMTagUtil
getSingleton()
Deprecated.use the static methods inSAMTag
insteadshort
makeBinaryTag(String tag)
Deprecated.useinstead
String
makeStringTag(short tag)
Deprecated.useSAMTag.makeStringTag(short)
instead
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Field Detail
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AM
@Deprecated public final short AM
Deprecated.useSAMTag.getBinaryTag()
instead.
-
AS
@Deprecated public final short AS
Deprecated.useSAMTag.getBinaryTag()
instead.
-
BC
@Deprecated public final short BC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
BQ
@Deprecated public final short BQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
BZ
@Deprecated public final short BZ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CB
@Deprecated public final short CB
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CC
@Deprecated public final short CC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CG
@Deprecated public final short CG
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CM
@Deprecated public final short CM
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CO
@Deprecated public final short CO
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CP
@Deprecated public final short CP
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CQ
@Deprecated public final short CQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CR
@Deprecated public final short CR
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CS
@Deprecated public final short CS
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CT
@Deprecated public final short CT
Deprecated.useSAMTag.getBinaryTag()
instead.
-
CY
@Deprecated public final short CY
Deprecated.useSAMTag.getBinaryTag()
instead.
-
E2
@Deprecated public final short E2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
FI
@Deprecated public final short FI
Deprecated.useSAMTag.getBinaryTag()
instead.
-
FS
@Deprecated public final short FS
Deprecated.useSAMTag.getBinaryTag()
instead.
-
FT
@Deprecated public final short FT
Deprecated.useSAMTag.getBinaryTag()
instead.
-
FZ
@Deprecated public final short FZ
Deprecated.useSAMTag.getBinaryTag()
instead.
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GC
@Deprecated public final short GC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
GS
@Deprecated public final short GS
Deprecated.useSAMTag.getBinaryTag()
instead.
-
GQ
@Deprecated public final short GQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
LB
@Deprecated public final short LB
Deprecated.useSAMTag.getBinaryTag()
instead.
-
H0
@Deprecated public final short H0
Deprecated.useSAMTag.getBinaryTag()
instead.
-
H1
@Deprecated public final short H1
Deprecated.useSAMTag.getBinaryTag()
instead.
-
H2
@Deprecated public final short H2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
HI
@Deprecated public final short HI
Deprecated.useSAMTag.getBinaryTag()
instead.
-
IH
@Deprecated public final short IH
Deprecated.useSAMTag.getBinaryTag()
instead.
-
MC
@Deprecated public final short MC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
MF
@Deprecated public final short MF
Deprecated.useSAMTag.getBinaryTag()
instead.
-
MI
@Deprecated public final short MI
Deprecated.useSAMTag.getBinaryTag()
instead.
-
MD
@Deprecated public final short MD
Deprecated.useSAMTag.getBinaryTag()
instead.
-
MQ
@Deprecated public final short MQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
NH
@Deprecated public final short NH
Deprecated.useSAMTag.getBinaryTag()
instead.
-
NM
@Deprecated public final short NM
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OQ
@Deprecated public final short OQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OP
@Deprecated public final short OP
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OC
@Deprecated public final short OC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OF
@Deprecated public final short OF
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OR
@Deprecated public final short OR
Deprecated.useSAMTag.getBinaryTag()
instead.
-
OX
@Deprecated public final short OX
Deprecated.useSAMTag.getBinaryTag()
instead.
-
PG
@Deprecated public final short PG
Deprecated.useSAMTag.getBinaryTag()
instead.
-
PQ
@Deprecated public final short PQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
PT
@Deprecated public final short PT
Deprecated.useSAMTag.getBinaryTag()
instead.
-
PU
@Deprecated public final short PU
Deprecated.useSAMTag.getBinaryTag()
instead.
-
QT
@Deprecated public final short QT
Deprecated.useSAMTag.getBinaryTag()
instead.
-
Q2
@Deprecated public final short Q2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
QX
@Deprecated public final short QX
Deprecated.useSAMTag.getBinaryTag()
instead.
-
R2
@Deprecated public final short R2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
RG
@Deprecated public final short RG
Deprecated.useSAMTag.getBinaryTag()
instead.
-
RT
@Deprecated public final short RT
Deprecated.useSAMTag.getBinaryTag()
instead.
-
RX
@Deprecated public final short RX
Deprecated.useSAMTag.getBinaryTag()
instead.
-
S2
@Deprecated public final short S2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
SA
@Deprecated public final short SA
Deprecated.useSAMTag.getBinaryTag()
instead.
-
SM
@Deprecated public final short SM
Deprecated.useSAMTag.getBinaryTag()
instead.
-
SQ
@Deprecated public final short SQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
TC
@Deprecated public final short TC
Deprecated.useSAMTag.getBinaryTag()
instead.
-
U2
@Deprecated public final short U2
Deprecated.useSAMTag.getBinaryTag()
instead.
-
UQ
@Deprecated public final short UQ
Deprecated.useSAMTag.getBinaryTag()
instead.
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Method Detail
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getSingleton
@Deprecated public static SAMTagUtil getSingleton()
Deprecated.use the static methods inSAMTag
insteadDespite the fact that this class has state, it should be thread-safe because the cache gets filled with the same values by any thread.
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makeBinaryTag
@Deprecated public short makeBinaryTag(String tag)
Deprecated.useinstead
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
@Deprecated public String makeStringTag(short tag)
Deprecated.useSAMTag.makeStringTag(short)
insteadConvert 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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