Class/Object

nl.biopet.utils.ngs.intervals

BedRecordList

Related Docs: object BedRecordList | package intervals

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case class BedRecordList(chrRecords: Map[String, List[BedRecord]], header: List[String] = Nil) extends Product with Serializable

Created by pjvan_thof on 8/20/15.

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Serializable, Serializable, Product, Equals, AnyRef, Any
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  1. BedRecordList
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
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Instance Constructors

  1. new BedRecordList(chrRecords: Map[String, List[BedRecord]], header: List[String] = Nil)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    AnyRef → Any

  4. def allRecords: Iterable[BedRecord]

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  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  6. val chrRecords: Map[String, List[BedRecord]]

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  7. def clone(): AnyRef

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

  8. def combineOverlap: BedRecordList

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

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    Definition Classes
    AnyRef

  10. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  11. def fractionOf(length: Long): Double

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    This return the fraction of the regions comparing to a length

  12. def fractionOfReference(file: File): Double

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    This return the fraction of the regions comparing to a reference

  13. def fractionOfReference(dict: SAMSequenceDictionary): Double

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    This return the fraction of the regions comparing to a reference

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

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    Definition Classes
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  15. def getGc(referenceFile: IndexedFastaSequenceFile): Double

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  16. val header: List[String]

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  17. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  18. lazy val isSorted: Boolean

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  19. def length: Long

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

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    Definition Classes
    AnyRef

  21. final def notify(): Unit

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    Definition Classes
    AnyRef

  22. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  23. def overlapWith(record: BedRecord): List[BedRecord]

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  24. def scatter(binSize: Int, combineContigs: Boolean = true, maxContigsInSingleJob: Option[Int] = None): List[List[BedRecord]]

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  25. lazy val sorted: BedRecordList

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  26. def squishBed(strandSensitive: Boolean = true, nameSensitive: Boolean = true): BedRecordList

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

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    Definition Classes
    AnyRef

  28. def toSamIntervals: Iterable[Interval]

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  29. def validateContigs(dict: SAMSequenceDictionary): BedRecordList

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  30. def validateContigs(reference: File): BedRecordList

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  31. final def wait(): Unit

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    Definition Classes
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    Annotations
    @throws( ... )

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

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    Definition Classes
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    @throws( ... )

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

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    Definition Classes
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    Annotations
    @throws( ... )

  34. def writeToFile(file: File): 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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