RealignmentTargetFinder

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

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9. def equals(arg0: Any): Boolean

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10. def finalize(): Unit

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

11. 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.

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 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.

17. 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.

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    @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.

18. def log: Logger

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

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20. def logDebug(msg: ⇒ String): Unit

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

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22. def logError(msg: ⇒ String): Unit

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

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24. def logInfo(msg: ⇒ String): Unit

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25. def logName: String

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

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27. def logTrace(msg: ⇒ String): Unit

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

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

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

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31. final def notify(): Unit

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32. final def notifyAll(): Unit

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

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34. def toString(): String

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35. final def wait(): Unit

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

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

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