RichAlignmentRecord

Value Members

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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   Definition Classes

   AnyRef

9. def equals(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

10. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

11. def fivePrimePosition: Option[Long]

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

    Definition Classes

    AnyRef → Any

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

14. def hashCode(): Int

    Definition Classes

    AnyRef → Any

15. lazy val illuminaOptics: Option[IlluminaOptics]

16. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

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

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

19. lazy val mdTag: Option[MdTag]

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

    Definition Classes

    AnyRef

21. final def notify(): Unit

    Definition Classes

    AnyRef

22. final def notifyAll(): Unit

    Definition Classes

    AnyRef

23. def overlapsReferencePosition(pos: ReferencePosition): Option[Boolean]

24. lazy val qualityScores: Array[Int]

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

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

27. lazy val readRegion: Option[ReferenceRegion]

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

    Definition Classes

    AnyRef

34. lazy val tags: Seq[Attribute]

35. def toString(): String

    Definition Classes

    AnyRef → Any

36. lazy val unclippedEnd: Option[Long]

37. lazy val unclippedStart: Option[Long]

38. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )