org.bdgenomics.adam.rich

# RichAlignmentRecord

#### class RichAlignmentRecord extends AnyRef

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### Instance Constructors

1. #### new RichAlignmentRecord(record: AlignmentRecord)

### 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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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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9. #### def fivePrimePosition: Long

10. #### def fivePrimeReferencePosition: ReferencePosition

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

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

13. #### def hashCode(): Int

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14. #### lazy val illuminaOptics: Option[IlluminaOptics]

15. #### final def isInstanceOf[T0]: Boolean

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

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

18. #### lazy val mdTag: Option[MdTag]

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

23. #### lazy val qualityScores: Array[Int]

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

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

26. #### val record: AlignmentRecord

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

28. #### lazy val referenceLength: Int

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

30. #### lazy val samtoolsCigar: Cigar

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

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32. #### lazy val tags: Seq[Attribute]

33. #### def toString(): String

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34. #### lazy val unclippedEnd: Long

35. #### lazy val unclippedStart: Long

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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