org.bdgenomics.adam.rdd.read.recalibration

Covariate

trait Covariate extends AnyRef

A Covariate represents a predictor, also known as a "feature" or "independent variable".

Note

Concrete implementations of Covariate should inherit from AbstractCovariate, not Covariate.

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Known Subclasses
AbstractCovariate, CycleCovariate, DinucCovariate
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Type Members

  1. abstract type Value

Abstract Value Members

  1. abstract def compute(read: DecadentRead): Seq[Option[Value]]

    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.

  2. abstract def csvFieldName: String

Concrete Value Members

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

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  2. final def ##(): Int

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

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

  5. final def asInstanceOf[T0]: T0

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  6. def clone(): AnyRef

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

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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

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  14. final def notify(): Unit

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  15. final def notifyAll(): Unit

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

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

  18. def toString(): String

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  19. final def wait(): Unit

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

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

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