Class

org.bdgenomics.adam.models

Coverage

Related Doc: package models

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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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Instance Constructors

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

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    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: 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. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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  6. val contigName: String

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    The chromosome that this coverage was observed on.

  7. val count: Double

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    The average coverage across this region.

  8. val end: Long

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

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

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  10. def finalize(): Unit

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

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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. val start: Long

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

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

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  18. def toFeature: Feature

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    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

  19. def toSqlFeature: Feature

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    Converts Coverage to a Feature case class, for use with Spark SQL.

  20. final def wait(): Unit

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

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

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Inherited from Serializable

Inherited from Serializable

Inherited from Product

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