Class/Object

nl.biopet.tools.mergesv

SvCall

Related Docs: object SvCall | package mergesv

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case class SvCall(contig1: String, pos1: Int, contig2: String, pos2: Int, svType: String, posCi: Interval, endCi: Interval, callers: List[String], orientation1: Boolean = true, orientation2: Boolean = true, existsInSamples: List[String] = Nil, callerFields: Map[String, Map[String, AnyRef]] = Map()) extends Logging with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, Logging, AnyRef, Any
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Inherited
  1. SvCall
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Logging
  7. AnyRef
  8. Any
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Visibility
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Instance Constructors

  1. new SvCall(contig1: String, pos1: Int, contig2: String, pos2: Int, svType: String, posCi: Interval, endCi: Interval, callers: List[String], orientation1: Boolean = true, orientation2: Boolean = true, existsInSamples: List[String] = Nil, callerFields: Map[String, Map[String, AnyRef]] = Map())

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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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. val callerFields: Map[String, Map[String, AnyRef]]

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  6. val callers: List[String]

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  7. def clone(): AnyRef

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

  8. val contig1: String

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  9. val contig2: String

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  10. val endCi: Interval

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

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    Definition Classes
    AnyRef

  12. val existsInSamples: List[String]

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  13. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  15. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  16. def logger: Logger

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    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  18. final def notify(): Unit

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    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  20. val orientation1: Boolean

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  21. val orientation2: Boolean

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  22. def overlapWith(other: SvCall): Boolean

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  23. val pos1: Int

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  24. val pos2: Int

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  25. val posCi: Interval

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  26. def referenceAllele(referenceReader: IndexedFastaSequenceFile): Allele

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  27. val svType: String

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

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    Definition Classes
    AnyRef

  29. def toVariantContext(referenceReader: IndexedFastaSequenceFile): VariantContext

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  30. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped