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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