org.bdgenomics.adam.rdd.pileup

PileupRDDFunctions

class PileupRDDFunctions extends Serializable with Logging

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Instance Constructors

  1. new PileupRDDFunctions(rdd: RDD[Pileup])

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. def adamPileupsToRods(coverage: Int = 30): RDD[Rod]

    Converts ungrouped pileup bases into reference grouped bases.

    Converts ungrouped pileup bases into reference grouped bases.

    coverage

    Coverage value is used to increase number of reducer operators.

    returns

    RDD with rods grouped by reference position.

  7. final def asInstanceOf[T0]: T0

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  8. def clone(): AnyRef

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

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  10. def equals(arg0: Any): Boolean

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  11. def finalize(): Unit

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

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  13. def hashCode(): Int

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  14. final def isInstanceOf[T0]: Boolean

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  15. def isTraceEnabled(): Boolean

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  16. def log: Logger

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

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

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

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

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

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

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  23. def logName: String

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

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

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

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

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

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  29. final def notify(): Unit

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  30. final def notifyAll(): Unit

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

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  32. def toString(): String

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  33. final def wait(): Unit

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

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

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