IndelRealignmentTarget

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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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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    protected[java.lang]

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

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

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12. def getIndelSet(): Set[IndelRange]

    Attributes

    protected[org.bdgenomics.adam.algorithms.realignmenttarget]

13. def getReadRange(): NumericRange[Long]

14. def getSNPSet(): Set[SNPRange]

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    protected[org.bdgenomics.adam.algorithms.realignmenttarget]

15. def getSortKey(): Long

16. def hashCode(): Int

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17. val indelSet: Set[IndelRange]

18. def isEmpty(): Boolean

19. final def isInstanceOf[T0]: Boolean

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20. def isTraceEnabled(): Boolean

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    protected

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    Logging

21. def log: Logger

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

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    protected

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23. def logDebug(msg: ⇒ String): Unit

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    protected

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

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    protected

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25. def logError(msg: ⇒ String): Unit

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    protected

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

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27. def logInfo(msg: ⇒ String): Unit

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    protected

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

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    protected

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29. def logTrace(msg: ⇒ String): Unit

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    protected

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    Logging

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

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    protected

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

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    protected

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    Logging

32. def merge(target: IndelRealignmentTarget): IndelRealignmentTarget

    Merges two indel realignment targets.

    Merges two indel realignment targets.

    target

    Target to merge in.

    returns

    Merged target.

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

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34. final def notify(): Unit

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35. final def notifyAll(): Unit

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36. def readRange: Inclusive[Long]

37. val snpSet: Set[SNPRange]

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

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39. def toString(): String

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40. final def wait(): Unit

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

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

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    @throws( ... )