Class ReadEnds

All Implemented Interfaces:
Serializable, PhysicalLocation
Direct Known Subclasses:
ReadEndsForMarkDuplicates, ReadEndsForMateCigar

public abstract class ReadEnds extends PhysicalLocationShort
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
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  • 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