Package picard.sam.markduplicates.util
Class ReadEnds
java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.util.PhysicalLocationShort
picard.sam.markduplicates.util.ReadEnds
- All Implemented Interfaces:
Serializable
,PhysicalLocation
- Direct Known Subclasses:
ReadEndsForMarkDuplicates
,ReadEndsForMateCigar
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final byte
static final byte
static final byte
boolean
A *transient* flag marking this read end as being an optical duplicate.short
byte
byte
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a matestatic final byte
int
int
int
int
short
static final byte
static final byte
Fields inherited from class picard.sam.util.PhysicalLocationInt
tile, x, y
Fields inherited from interface picard.sam.util.PhysicalLocation
NO_VALUE
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionshort
static byte
getOrientationByte
(boolean read1NegativeStrand, boolean read2NegativeStrand) Returns a single byte that encodes the orientation of the two reads in a pair.short
boolean
isPaired()
void
setLibraryId
(short libraryId) void
setReadGroup
(short readGroup) Methods inherited from class picard.sam.util.PhysicalLocationShort
setX, setY
Methods inherited from class picard.sam.util.PhysicalLocationInt
getTile, getX, getY, setTile
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface picard.sam.util.PhysicalLocation
hasLocation
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Field Details
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F
public static final byte F- See Also:
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R
public static final byte R- See Also:
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FF
public static final byte FF- See Also:
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FR
public static final byte FR- See Also:
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RR
public static final byte RR- See Also:
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RF
public static final byte RF- See Also:
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libraryId
public short libraryId -
orientation
public byte orientation -
read1ReferenceIndex
public int read1ReferenceIndex -
read1Coordinate
public int read1Coordinate -
read2ReferenceIndex
public int read2ReferenceIndex -
read2Coordinate
public int read2Coordinate -
readGroup
public short readGroup -
orientationForOpticalDuplicates
public byte orientationForOpticalDuplicatesFor optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate -
isOpticalDuplicate
public transient boolean isOpticalDuplicateA *transient* flag marking this read end as being an optical duplicate.
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Constructor Details
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ReadEnds
public ReadEnds()
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Method Details
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isPaired
public boolean isPaired() -
getReadGroup
public short getReadGroup()- Specified by:
getReadGroup
in interfacePhysicalLocation
- Overrides:
getReadGroup
in classPhysicalLocationInt
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setReadGroup
public void setReadGroup(short readGroup) - Specified by:
setReadGroup
in interfacePhysicalLocation
- Overrides:
setReadGroup
in classPhysicalLocationInt
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getLibraryId
public short getLibraryId()- Specified by:
getLibraryId
in interfacePhysicalLocation
- Overrides:
getLibraryId
in classPhysicalLocationInt
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setLibraryId
public void setLibraryId(short libraryId) - Specified by:
setLibraryId
in interfacePhysicalLocation
- Overrides:
setLibraryId
in classPhysicalLocationInt
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getOrientationByte
public static byte getOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand) Returns a single byte that encodes the orientation of the two reads in a pair.
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