Class/Object

org.bdgenomics.adam.rich

RichAlignmentRecord

Related Docs: object RichAlignmentRecord | package rich

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class RichAlignmentRecord extends AnyRef

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Instance Constructors

  1. new RichAlignmentRecord(record: AlignmentRecord)

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Value Members

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

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

  9. def fivePrimePosition: Long

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  10. def fivePrimeReferencePosition: ReferencePosition

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

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

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  13. def hashCode(): Int

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  14. lazy val illuminaOptics: Option[IlluminaOptics]

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  15. final def isInstanceOf[T0]: Boolean

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

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

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  18. lazy val mdTag: Option[MdTag]

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

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  20. final def notify(): Unit

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  21. final def notifyAll(): Unit

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  22. def overlapsReferencePosition(pos: ReferencePosition): Boolean

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  23. lazy val qualityScores: Array[Int]

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

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

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  26. val record: AlignmentRecord

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

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  28. lazy val referenceLength: Int

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

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  30. lazy val samtoolsCigar: Cigar

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

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  32. lazy val tags: Seq[Attribute]

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  33. def toString(): String

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  34. lazy val unclippedEnd: Long

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  35. lazy val unclippedStart: Long

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  36. final def wait(): Unit

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

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

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