Package picard.sam.util

Interface PhysicalLocation

All Superinterfaces:
Serializable
All Known Implementing Classes:
PhysicalLocationForMateCigar, PhysicalLocationInt, PhysicalLocationShort, ReadEnds, ReadEndsForMarkDuplicates, ReadEndsForMarkDuplicatesWithBarcodes, ReadEndsForMateCigar
public interface PhysicalLocation extends Serializable
Small interface that provides access to the physical location information about a cluster. All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow non-zero positive integers, x and y coordinates may be negative.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    NO_VALUE
     

  • Method Summary

    Modifier and Type
    Method
    Description
    short
    getLibraryId()
     
    short
    getReadGroup()
     
    short
    getTile()
     
    int
    getX()
     
    int
    getY()
     
    default boolean
    hasLocation()
    Default implementation of a method to check whether real location data has been set.
    void
    setLibraryId(short libraryId)
     
    void
    setReadGroup(short rg)
     
    void
    setTile(short tile)
     
    void
    setX(int x)
     
    void
    setY(int y)
     

  • Field Details

  • Method Details

    • getReadGroup

      short getReadGroup()

    • setReadGroup

      void setReadGroup(short rg)

    • getTile

      short getTile()

    • setTile

      void setTile(short tile)

    • getX

      int getX()

    • setX

      void setX(int x)

    • getY

      int getY()

    • setY

      void setY(int y)

    • getLibraryId

      short getLibraryId()

    • setLibraryId

      void setLibraryId(short libraryId)

    • hasLocation

      default boolean hasLocation()
      Default implementation of a method to check whether real location data has been set.