org.bdgenomics.adam.rdd.read.recalibration

CycleCovariate

class CycleCovariate extends AbstractCovariate[Int]

Linear Supertypes
AbstractCovariate[Int], Serializable, Serializable, Covariate, AnyRef, Any
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Inherited
  1. CycleCovariate
  2. AbstractCovariate
  3. Serializable
  4. Serializable
  5. Covariate
  6. AnyRef
  7. Any
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Instance Constructors

  1. new CycleCovariate()

Type Members

  1. type Value = Int

    Definition Classes
    AbstractCovariate → Covariate

Value Members

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

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef → Any

  4. def apply(read: DecadentRead): Seq[Option[Value]]

    Definition Classes
    Covariate

  5. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  6. def clone(): AnyRef

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

  7. def compute(read: DecadentRead): Seq[Option[Int]]

    Given a read, computes the value of this covariate for each residue in the read.

    Given a read, computes the value of this covariate for each residue in the read.

    The returned values must be in the same order as the residues. A value of None means this covariate does not apply to the corresponding residue.

    Example: The DinucCovariate returns a pair of bases for each residue, except for bases at the start of a read, for which it returns None.

    Definition Classes
    CycleCovariate → Covariate

  8. def csvFieldName: String

    Definition Classes
    CycleCovariate → Covariate

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

    Definition Classes
    AnyRef

  10. def equals(other: Any): Boolean

    Definition Classes
    CycleCovariate → AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

    Definition Classes
    CycleCovariate → AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    AnyRef

  19. def toCSV(option: Option[Value]): String

    Definition Classes
    Covariate

  20. def toString(): String

    Definition Classes
    AnyRef → Any

  21. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AbstractCovariate[Int]

Inherited from Serializable

Inherited from Serializable

Inherited from Covariate

Inherited from AnyRef

Inherited from Any

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