Package picard.sam.markduplicates.util
Class ReadEndsForMarkDuplicates
java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.util.PhysicalLocationShort
picard.sam.markduplicates.util.ReadEnds
picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- All Implemented Interfaces:
Serializable
,Cloneable
,PhysicalLocation
- Direct Known Subclasses:
ReadEndsForMarkDuplicatesWithBarcodes
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionint
long
long
short
protected static final int
Fields inherited from class picard.sam.markduplicates.util.ReadEnds
F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR
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
ConstructorsConstructorDescription -
Method Summary
Modifier and TypeMethodDescriptionclone()
static int
static boolean
isSingleEndReadKnownFragment
(htsjdk.samtools.SAMRecord rec) This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e.toString()
Methods inherited from class picard.sam.markduplicates.util.ReadEnds
getLibraryId, getOrientationByte, getReadGroup, isPaired, setLibraryId, setReadGroup
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
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface picard.sam.util.PhysicalLocation
hasLocation
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Field Details
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SIZE_OF
protected static final int SIZE_OF- See Also:
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score
public short score -
read1IndexInFile
public long read1IndexInFile -
read2IndexInFile
public long read2IndexInFile -
duplicateSetSize
public int duplicateSetSize
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Constructor Details
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ReadEndsForMarkDuplicates
public ReadEndsForMarkDuplicates() -
ReadEndsForMarkDuplicates
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Method Details
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getSizeOf
public static int getSizeOf() -
toString
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clone
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isSingleEndReadKnownFragment
public static boolean isSingleEndReadKnownFragment(htsjdk.samtools.SAMRecord rec) This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e. it was not quality trimmed)
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