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.
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final bytestatic final bytestatic final bytebooleanA *transient* flag marking this read end as being an optical duplicate.shortbytebyteFor optical duplicate detection the orientation matters regard to 1st or 2nd end of a matestatic final byteintintintintshortstatic final bytestatic final byteFields inherited from class picard.sam.util.PhysicalLocationInt
tile, x, yFields inherited from interface picard.sam.util.PhysicalLocation
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionshortstatic bytegetOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand) Returns a single byte that encodes the orientation of the two reads in a pair.shortbooleanisPaired()voidsetLibraryId(short libraryId) voidsetReadGroup(short readGroup) Methods inherited from class picard.sam.util.PhysicalLocationShort
setX, setYMethods inherited from class picard.sam.util.PhysicalLocationInt
getTile, getX, getY, setTileMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods 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:
getReadGroupin interfacePhysicalLocation- Overrides:
getReadGroupin classPhysicalLocationInt
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setReadGroup
public void setReadGroup(short readGroup) - Specified by:
setReadGroupin interfacePhysicalLocation- Overrides:
setReadGroupin classPhysicalLocationInt
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getLibraryId
public short getLibraryId()- Specified by:
getLibraryIdin interfacePhysicalLocation- Overrides:
getLibraryIdin classPhysicalLocationInt
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setLibraryId
public void setLibraryId(short libraryId) - Specified by:
setLibraryIdin interfacePhysicalLocation- Overrides:
setLibraryIdin 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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