org.bdgenomics.adam.rdd.variation

GenotypeRDDFunctions

class GenotypeRDDFunctions extends Serializable with Logging

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Instance Constructors

  1. new GenotypeRDDFunctions(rdd: RDD[Genotype])

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
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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. def concordanceWith(truth: RDD[Genotype]): RDD[(String, ConcordanceTable)]

    Compute the per-sample ConcordanceTable for this genotypes vs.

    Compute the per-sample ConcordanceTable for this genotypes vs. the supplied truth dataset. Only genotypes with ploidy <= 2 will be considered.

    truth

    Truth genotypes

    returns

    PairedRDD of sample -> ConcordanceTable

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def filterByOverlappingRegion(query: ReferenceRegion): RDD[Genotype]

  12. def finalize(): Unit

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

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

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  14. def hashCode(): Int

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  15. final def isInstanceOf[T0]: Boolean

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  16. def isTraceEnabled(): Boolean

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    protected
    Definition Classes
    Logging

  17. def log: Logger

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    Logging

  18. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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  19. def logDebug(msg: ⇒ String): Unit

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    Definition Classes
    Logging

  20. def logError(msg: ⇒ String, throwable: Throwable): Unit

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  21. def logError(msg: ⇒ String): Unit

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  22. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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  23. def logInfo(msg: ⇒ String): Unit

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  24. def logName: String

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  25. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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  26. def logTrace(msg: ⇒ String): Unit

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  27. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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  28. def logWarning(msg: ⇒ String): Unit

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    Definition Classes
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  29. final def ne(arg0: AnyRef): Boolean

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  30. final def notify(): Unit

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  31. final def notifyAll(): Unit

    Definition Classes
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  32. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
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  33. def toString(): String

    Definition Classes
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  34. def toVariantContext(): RDD[VariantContext]

  35. final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

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

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Inherited from Logging

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Inherited from AnyRef

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