Package picard.sam.markduplicates.util
Class ReadEndsForMarkDuplicates
- java.lang.Object
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- picard.sam.util.PhysicalLocationInt
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- picard.sam.util.PhysicalLocationShort
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- picard.sam.markduplicates.util.ReadEnds
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- picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
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- All Implemented Interfaces:
Serializable
,Cloneable
,PhysicalLocation
- Direct Known Subclasses:
ReadEndsForMarkDuplicatesWithBarcodes
public class ReadEndsForMarkDuplicates extends ReadEnds implements Cloneable
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description int
duplicateSetSize
long
read1IndexInFile
long
read2IndexInFile
short
score
protected static int
SIZE_OF
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Fields inherited from class picard.sam.markduplicates.util.ReadEnds
F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR
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Fields inherited from class picard.sam.util.PhysicalLocationInt
tile, x, y
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Fields inherited from interface picard.sam.util.PhysicalLocation
NO_VALUE
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Constructor Summary
Constructors Constructor Description ReadEndsForMarkDuplicates()
ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description ReadEndsForMarkDuplicates
clone()
static int
getSizeOf()
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Methods inherited from class picard.sam.markduplicates.util.ReadEnds
getLibraryId, getOrientationByte, getReadGroup, isPaired, setLibraryId, setReadGroup
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Methods inherited from class picard.sam.util.PhysicalLocationShort
setX, setY
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Methods inherited from class picard.sam.util.PhysicalLocationInt
getTile, getX, getY, setTile
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface picard.sam.util.PhysicalLocation
hasLocation
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Field Detail
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SIZE_OF
protected static final int SIZE_OF
- See Also:
- Constant Field Values
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score
public short score
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read1IndexInFile
public long read1IndexInFile
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read2IndexInFile
public long read2IndexInFile
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duplicateSetSize
public int duplicateSetSize
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Constructor Detail
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ReadEndsForMarkDuplicates
public ReadEndsForMarkDuplicates()
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ReadEndsForMarkDuplicates
public ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)
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Method Detail
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getSizeOf
public static int getSizeOf()
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clone
public ReadEndsForMarkDuplicates clone()
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