org.bdgenomics.adam.models

Rod

case class Rod(position: ReferencePosition, pileups: List[Pileup]) extends Product with Serializable

Class representing a set of pileup bases at a specific locus.

position

Position on the reference genome.

pileups

A list representing the bases at this locus.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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  1. Rod
  2. Serializable
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Instance Constructors

  1. new Rod(position: ReferencePosition, pileups: List[Pileup])

    position

    Position on the reference genome.

    pileups

    A list representing the bases at this locus.

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  8. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  9. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  10. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  11. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  12. lazy val isSingleSample: Boolean

  13. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  14. final def notify(): Unit

    Definition Classes
    AnyRef

  15. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  16. val pileups: List[Pileup]

    A list representing the bases at this locus.

  17. val position: ReferencePosition

    Position on the reference genome.

  18. def splitBySamples(): List[Rod]

    Splits this rod out by samples.

    Splits this rod out by samples.

    returns

    A list of rods, each corresponding to a single sample.

  19. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  20. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  21. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
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    @throws( ... )

  22. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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