org.bdgenomics.adam.rdd.read.realignment

RealignmentTargetFinder

class RealignmentTargetFinder extends Serializable with Logging

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Instance Constructors

  1. new RealignmentTargetFinder()

Value Members

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

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    AnyRef → Any
  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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    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean

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  7. def equals(arg0: Any): Boolean

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  8. def finalize(): Unit

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    @throws( classOf[java.lang.Throwable] )
  9. def findTargets(reads: RDD[RichAlignmentRecord], maxIndelSize: Int = 500, maxTargetSize: Int = 3000): TargetSet

    Finds indel targets over a set of reads.

    Finds indel targets over a set of reads.

    reads

    An RDD containing reads to generate indel realignment targets from.

    returns

    An ordered set of indel realignment targets.

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

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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  13. def isTraceEnabled(): Boolean

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    protected
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    Logging
  14. def joinTargets(first: TargetSet, second: TargetSet): TargetSet

    Wrapper for joinTargets(TreeSet[IndelRealignmentTarget], TreeSet[IndelRealignmentTarget]) for contexts where serialization is needed.

    Wrapper for joinTargets(TreeSet[IndelRealignmentTarget], TreeSet[IndelRealignmentTarget]) for contexts where serialization is needed.

    first

    A sorted set of realignment targets. This set must be ordered ahead of the second set.

    second

    A sorted set of realignment targets.

    returns

    A merged set of targets.

  15. final def joinTargets(first: TreeSet[IndelRealignmentTarget], second: TreeSet[IndelRealignmentTarget]): TreeSet[IndelRealignmentTarget]

    Joins two sorted sets of targets together.

    Joins two sorted sets of targets together. Is tail call recursive.

    first

    A sorted set of realignment targets. This set must be ordered ahead of the second set.

    second

    A sorted set of realignment targets.

    returns

    A merged set of targets.

    Attributes
    protected
    Annotations
    @tailrec()
    Note

    This function should not be called in a context where target set serialization is needed. Instead, call joinTargets(TargetSet, TargetSet), which wraps this function.

  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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Inherited from Logging

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