Package picard.sam.markduplicates.util
Class ReadEndsForMateCigar
java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.util.PhysicalLocationShort
picard.sam.markduplicates.util.ReadEnds
picard.sam.markduplicates.util.ReadEndsForMateCigar
- All Implemented Interfaces:
Serializable
,PhysicalLocation
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.
- See Also:
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Field Summary
FieldsFields 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
ConstructorsConstructorDescriptionReadEndsForMateCigar
(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" -
Method Summary
Modifier and TypeMethodDescriptionGets the read ends for optical duplicate trackinghtsjdk.samtools.SAMRecord
htsjdk.samtools.util.SamRecordWithOrdinal
A number of convenience functionsboolean
isPaired()
void
setLocationSet
(PhysicalLocationForMateCigarSet locationSet) Methods inherited from class picard.sam.markduplicates.util.ReadEnds
getLibraryId, getOrientationByte, getReadGroup, 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
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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samRecordWithOrdinal
public htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal
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Constructor Details
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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. -
ReadEndsForMateCigar
public ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal) Creates a shallow copy from the "other"
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Method Details
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getSamRecordIndex
public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()A number of convenience functions -
getRecord
public htsjdk.samtools.SAMRecord getRecord() -
getRecordReadName
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isPaired
public boolean isPaired() -
getReadEndSetForOpticalDuplicates
Gets the read ends for optical duplicate tracking -
getLocationSet
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removeLocationSet
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setLocationSet
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