Package htsjdk.samtools
Class SAMTagUtil
java.lang.Object
htsjdk.samtools.SAMTagUtil
Deprecated.
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
Modifier and TypeFieldDescriptionfinal short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead.final short
Deprecated.useSAMTag.getBinaryTag()
instead. -
Constructor Summary
-
Method Summary
Modifier and TypeMethodDescriptionstatic SAMTagUtil
Deprecated.use the static methods inSAMTag
insteadshort
makeBinaryTag
(String tag) Deprecated.useinstead
makeStringTag
(short tag) Deprecated.useSAMTag.makeStringTag(short)
instead
-
Field Details
-
AM
Deprecated.useSAMTag.getBinaryTag()
instead. -
AS
Deprecated.useSAMTag.getBinaryTag()
instead. -
BC
Deprecated.useSAMTag.getBinaryTag()
instead. -
BQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
BZ
Deprecated.useSAMTag.getBinaryTag()
instead. -
CB
Deprecated.useSAMTag.getBinaryTag()
instead. -
CC
Deprecated.useSAMTag.getBinaryTag()
instead. -
CG
Deprecated.useSAMTag.getBinaryTag()
instead. -
CM
Deprecated.useSAMTag.getBinaryTag()
instead. -
CO
Deprecated.useSAMTag.getBinaryTag()
instead. -
CP
Deprecated.useSAMTag.getBinaryTag()
instead. -
CQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
CR
Deprecated.useSAMTag.getBinaryTag()
instead. -
CS
Deprecated.useSAMTag.getBinaryTag()
instead. -
CT
Deprecated.useSAMTag.getBinaryTag()
instead. -
CY
Deprecated.useSAMTag.getBinaryTag()
instead. -
E2
Deprecated.useSAMTag.getBinaryTag()
instead. -
FI
Deprecated.useSAMTag.getBinaryTag()
instead. -
FS
Deprecated.useSAMTag.getBinaryTag()
instead. -
FT
Deprecated.useSAMTag.getBinaryTag()
instead. -
FZ
Deprecated.useSAMTag.getBinaryTag()
instead. -
GC
Deprecated.useSAMTag.getBinaryTag()
instead. -
GS
Deprecated.useSAMTag.getBinaryTag()
instead. -
GQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
LB
Deprecated.useSAMTag.getBinaryTag()
instead. -
H0
Deprecated.useSAMTag.getBinaryTag()
instead. -
H1
Deprecated.useSAMTag.getBinaryTag()
instead. -
H2
Deprecated.useSAMTag.getBinaryTag()
instead. -
HI
Deprecated.useSAMTag.getBinaryTag()
instead. -
IH
Deprecated.useSAMTag.getBinaryTag()
instead. -
MC
Deprecated.useSAMTag.getBinaryTag()
instead. -
MF
Deprecated.useSAMTag.getBinaryTag()
instead. -
MI
Deprecated.useSAMTag.getBinaryTag()
instead. -
MD
Deprecated.useSAMTag.getBinaryTag()
instead. -
MQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
NH
Deprecated.useSAMTag.getBinaryTag()
instead. -
NM
Deprecated.useSAMTag.getBinaryTag()
instead. -
OQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
OP
Deprecated.useSAMTag.getBinaryTag()
instead. -
OC
Deprecated.useSAMTag.getBinaryTag()
instead. -
OF
Deprecated.useSAMTag.getBinaryTag()
instead. -
OR
Deprecated.useSAMTag.getBinaryTag()
instead. -
OX
Deprecated.useSAMTag.getBinaryTag()
instead. -
PG
Deprecated.useSAMTag.getBinaryTag()
instead. -
PQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
PT
Deprecated.useSAMTag.getBinaryTag()
instead. -
PU
Deprecated.useSAMTag.getBinaryTag()
instead. -
QT
Deprecated.useSAMTag.getBinaryTag()
instead. -
Q2
Deprecated.useSAMTag.getBinaryTag()
instead. -
QX
Deprecated.useSAMTag.getBinaryTag()
instead. -
R2
Deprecated.useSAMTag.getBinaryTag()
instead. -
RG
Deprecated.useSAMTag.getBinaryTag()
instead. -
RT
Deprecated.useSAMTag.getBinaryTag()
instead. -
RX
Deprecated.useSAMTag.getBinaryTag()
instead. -
S2
Deprecated.useSAMTag.getBinaryTag()
instead. -
SA
Deprecated.useSAMTag.getBinaryTag()
instead. -
SM
Deprecated.useSAMTag.getBinaryTag()
instead. -
SQ
Deprecated.useSAMTag.getBinaryTag()
instead. -
TC
Deprecated.useSAMTag.getBinaryTag()
instead. -
U2
Deprecated.useSAMTag.getBinaryTag()
instead. -
UQ
Deprecated.useSAMTag.getBinaryTag()
instead.
-
-
Constructor Details
-
SAMTagUtil
public SAMTagUtil()Deprecated.
-
-
Method Details
-
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. -
makeBinaryTag
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.
-
makeStringTag
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.
-
SAMTag
enum.