org.bdgenomics.quinine.metrics.coverage

CoverageStats

case class CoverageStats(median: Double, mean: Double, distribution: Map[Int, Int]) extends Product with Serializable

Simple statistics about coverage.

median

The median coverage of a set of sites.

mean

The (arithmetic) mean coverage of a set of sites.

distribution

A map between coverage and the number of sites covered at that coverage.

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Instance Constructors

  1. new CoverageStats(median: Double, mean: Double, distribution: Map[Int, Int])

    median

    The median coverage of a set of sites.

    mean

    The (arithmetic) mean coverage of a set of sites.

    distribution

    A map between coverage and the number of sites covered at that coverage.

Value Members

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

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

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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

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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )

  8. val distribution: Map[Int, Int]

    A map between coverage and the number of sites covered at that coverage.

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

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  10. def finalize(): Unit

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

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

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  12. final def isInstanceOf[T0]: Boolean

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  13. val mean: Double

    The (arithmetic) mean coverage of a set of sites.

  14. val median: Double

    The median coverage of a set of sites.

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

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  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
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  18. def percentSitesCoveredAt(threshold: Int): Double

    Returns the percentage of sites with coverage higher than a threshold.

    Returns the percentage of sites with coverage higher than a threshold.

    threshold

    The coverage threshold.

    returns

    Returns the percentage of sites that are covered by more observations than this threshold value.

    See also

    sitesCoveredAt

  19. def sitesCoveredAt(threshold: Int): Int

    Returns the number of sites with coverage higher than a threshold.

    Returns the number of sites with coverage higher than a threshold.

    threshold

    The coverage threshold.

    returns

    Returns the number of sites that are covered by more observations than this threshold value.

    See also

    percentSitesCoveredAt

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

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  21. final def wait(): Unit

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

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

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