Class

org.biodatageeks.sequila.pileup.model

ContigAggregate

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case class ContigAggregate(contig: String = "", contigLen: Int = 0, events: Array[Short], alts: MultiLociAlts, quals: MultiLociQuals, startPosition: Int = 0, maxPosition: Int = 0, shrinkedEventsArraySize: Int = 0, maxSeqLen: Int = 0, qualityCache: QualityCache) extends Product with Serializable

Events aggregation on contig

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Serializable, Serializable, Product, Equals, AnyRef, Any
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Instance Constructors

  1. new ContigAggregate(contig: String = "", contigLen: Int = 0, events: Array[Short], alts: MultiLociAlts, quals: MultiLociQuals, startPosition: Int = 0, maxPosition: Int = 0, shrinkedEventsArraySize: Int = 0, maxSeqLen: Int = 0, qualityCache: QualityCache)

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Value Members

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

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    AnyRef → Any

  2. final def ##(): Int

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

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  4. def addToCache(readQualSummary: ReadQualSummary): Unit

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  5. val alts: MultiLociAlts

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  6. val altsKeyCache: TreeSet[Int]

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  7. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  8. def calculateAdjustedQuals(upd: PartitionCorrections): MultiLociQuals

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  9. def calculateMaxLength(allPositions: Boolean): Int

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  10. def clone(): AnyRef

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    Attributes
    protected[java.lang]
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    Annotations
    @throws( ... )

  11. val contig: String

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  12. val contigLen: Int

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

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    Definition Classes
    AnyRef

  14. val events: Array[Short]

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  15. def fillQualityForHigherAlts(upd: PartitionCorrections, adjustedQuals: MultiLociQuals, blacklist: Set[Int]): MultiLociQuals

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  16. def fillQualityForLowerAlts(upd: PartitionCorrections, qualsInterim: MultiLociQuals, blacklist: Set[Int]): MultiLociQuals

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  17. def finalize(): Unit

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

  18. def getAdjustedAggregate(b: Broadcast[FullCorrections]): ContigAggregate

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  19. def getAltPositionsForRange(start: Int, end: Int): SortedSet[Int]

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

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    Definition Classes
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  21. def getPileupUpdate: PileupUpdate

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  22. def getRange: Range

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  23. def getTail: Tail

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  24. def hasAltOnPosition(pos: Int): Boolean

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  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  26. val maxPosition: Int

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  27. val maxSeqLen: Int

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

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    Definition Classes
    AnyRef

  29. final def notify(): Unit

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    Definition Classes
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  30. final def notifyAll(): Unit

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    Definition Classes
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  31. val qualityCache: QualityCache

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  32. val quals: MultiLociQuals

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  33. val shrinkedEventsArraySize: Int

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  34. val startPosition: Int

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

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    Definition Classes
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  36. def trimQuals: MultiLociQuals

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  37. def updateAlts(pos: Int, alt: Char): Unit

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  38. def updateEvents(pos: Int, startPart: Int, delta: Short): Unit

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  39. def updateQuals(pos: Int, alt: Char, quality: Byte, firstUpdate: Boolean = false, updateMax: Boolean = true): Unit

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  40. final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

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

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Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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