RichAlignmentRecord

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. def fivePrimePosition: Long

12. def fivePrimeReferencePosition: ReferencePosition

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

    Definition Classes

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14. def getReferenceContext(readOffset: Int, referencePosition: Long, cigarElem: CigarElement, elemOffset: Int): ReferenceSequenceContext

15. def hashCode(): Int

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16. lazy val illuminaOptics: Option[IlluminaOptics]

17. final def isInstanceOf[T0]: Boolean

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18. def isMismatchAtReadOffset(offset: Int): Option[Boolean]

19. def isMismatchAtReferencePosition(pos: ReferencePosition): Option[Boolean]

20. lazy val mdTag: Option[MdTag]

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

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22. final def notify(): Unit

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23. final def notifyAll(): Unit

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24. def overlapsReferencePosition(pos: ReferencePosition): Boolean

25. lazy val qualityScores: Array[Int]

26. def readOffsetToReferencePosition(offset: Int): Option[ReferencePosition]

27. def readOffsetToReferenceSequenceContext(offset: Int): Option[ReferenceSequenceContext]

28. val record: AlignmentRecord

29. lazy val referenceContexts: Seq[Option[ReferenceSequenceContext]]

30. lazy val referenceLength: Int

31. lazy val referencePositions: Seq[Option[ReferencePosition]]

32. lazy val samtoolsCigar: Cigar

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

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34. lazy val tags: Seq[Attribute]

35. def toString(): String

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36. lazy val unclippedEnd: Long

37. lazy val unclippedStart: Long

38. final def wait(): Unit

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

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

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