Class ReadEnds

java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.markduplicates.util.ReadEnds
All Implemented Interfaces:
Serializable, PhysicalLocation
Direct Known Subclasses:
ReadEndsForMarkDuplicates, ReadEndsForMateCigar
public abstract class ReadEnds extends PhysicalLocationInt
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
See Also:

  • Field Details

    • F

      public static final byte F
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    • R

      public static final byte R
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    • FF

      public static final byte FF
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    • FR

      public static final byte FR
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    • RR

      public static final byte RR
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    • RF

      public static final byte RF
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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 orientationForOpticalDuplicates
      For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate

    • isOpticalDuplicate

      public transient boolean isOpticalDuplicate
      A *transient* flag marking this read end as being an optical duplicate.

  • Constructor Details

    • ReadEnds

      public ReadEnds()

  • Method Details