Package picard.sam.markduplicates.util
Class ReadEndsForMateCigar
- 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.ReadEndsForMateCigar
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- All Implemented Interfaces:
PhysicalLocation
public class ReadEndsForMateCigar extends ReadEnds
A class to store individual records for MarkDuplicatesWithMateCigar. This aids in comparing records to determine which need to be compared when we mark duplicates. We also store the original SAMRecord and its ordinal in the input file (in SamRecordWithOrdinal) to access optional tags (mate cigar) and other information.
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Field Summary
Fields Modifier and Type Field Description htsjdk.samtools.util.SamRecordWithOrdinalsamRecordWithOrdinal-
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 ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal, OpticalDuplicateFinder opticalDuplicateFinder, short libraryId)Builds a read ends object that represents a single read.ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)Creates a shallow copy from the "other"
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description PhysicalLocationForMateCigarSetgetLocationSet()Set<ReadEnds>getReadEndSetForOpticalDuplicates()Gets the read ends for optical duplicate trackinghtsjdk.samtools.SAMRecordgetRecord()StringgetRecordReadName()htsjdk.samtools.util.SamRecordWithOrdinalgetSamRecordIndex()A number of convenience functionsbooleanisPaired()PhysicalLocationForMateCigarSetremoveLocationSet()voidsetLocationSet(PhysicalLocationForMateCigarSet locationSet)-
Methods inherited from class picard.sam.markduplicates.util.ReadEnds
getLibraryId, getOrientationByte, getReadGroup, 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
clone, 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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Constructor Detail
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ReadEndsForMateCigar
public ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal, OpticalDuplicateFinder opticalDuplicateFinder, short libraryId)Builds a read ends object that represents a single read.
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ReadEndsForMateCigar
public ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)
Creates a shallow copy from the "other"
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Method Detail
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getSamRecordIndex
public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()
A number of convenience functions
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getRecord
public htsjdk.samtools.SAMRecord getRecord()
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getRecordReadName
public String getRecordReadName()
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getReadEndSetForOpticalDuplicates
public Set<ReadEnds> getReadEndSetForOpticalDuplicates()
Gets the read ends for optical duplicate tracking
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getLocationSet
public PhysicalLocationForMateCigarSet getLocationSet()
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removeLocationSet
public PhysicalLocationForMateCigarSet removeLocationSet()
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setLocationSet
public void setLocationSet(PhysicalLocationForMateCigarSet locationSet)
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