org.bdgenomics.adam.models

Coverage

case class Coverage(contigName: String, start: Long, end: Long, count: Double) extends Product with Serializable

Coverage record for CoverageRDD.

Contains Region indexed by contig name, start and end, as well as the average coverage at each base pair in that region.

contigName

The chromosome that this coverage was observed on.

start

The start coordinate of the region where this coverage value was observed.

end

The end coordinate of the region where this coverage value was observed.

count

The average coverage across this region.

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Serializable, Serializable, Product, Equals, AnyRef, Any
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Instance Constructors

  1. new Coverage(contigName: String, start: Long, end: Long, count: Double)

    contigName

    The chromosome that this coverage was observed on.

    start

    The start coordinate of the region where this coverage value was observed.

    end

    The end coordinate of the region where this coverage value was observed.

    count

    The average coverage across this region.

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
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  7. def clone(): AnyRef

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

  8. val contigName: String

    The chromosome that this coverage was observed on.

  9. val count: Double

    The average coverage across this region.

  10. val end: Long

    The end coordinate of the region where this coverage value was observed.

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

    Definition Classes
    AnyRef

  12. def finalize(): Unit

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

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

    Definition Classes
    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. val start: Long

    The start coordinate of the region where this coverage value was observed.

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

    Definition Classes
    AnyRef

  20. def toFeature: Feature

    Converts Coverage to Feature, setting Coverage count in the score attribute.

    Converts Coverage to Feature, setting Coverage count in the score attribute.

    returns

    Feature built from Coverage

  21. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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