Class/Object

nl.biopet.tools.digenicsearch

Variant

Related Docs: object Variant | package digenicsearch

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case class Variant(contig: Int, pos: Int, alleles: List[String], genotypes: List[Genotype], annotations: List[AnnotationValue] = List(), genotypeAnnotation: List[GenotypeAnnotation], detectionResult: DetectionResult, externalGenotypes: Array[List[Genotype]], externalDetectionResult: Array[DetectionResult], regionsIdx: Int) extends Product with Serializable

This stores a variant and genotypes in a compressed format

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

  1. new Variant(contig: Int, pos: Int, alleles: List[String], genotypes: List[Genotype], annotations: List[AnnotationValue] = List(), genotypeAnnotation: List[GenotypeAnnotation], detectionResult: DetectionResult, externalGenotypes: Array[List[Genotype]], externalDetectionResult: Array[DetectionResult], regionsIdx: Int)

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

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  4. val alleles: List[String]

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  5. val annotations: List[AnnotationValue]

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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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

  8. val contig: Int

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  9. val detectionResult: DetectionResult

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

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    Definition Classes
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  11. val externalDetectionResult: Array[DetectionResult]

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  12. val externalGenotypes: Array[List[Genotype]]

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  13. def filterExternalFractions(broadcasts: Broadcasts): Option[Variant]

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    This will remove filter variants on external fractions set on the commandline

  14. def filterFamilyFractions(broadcasts: Broadcasts, familyId: Option[Int] = None): Option[Variant]

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    Filter based on family fractions, usingOtherFamilies argument is used here

  15. def filterSingleFraction(broadcasts: Broadcasts): Option[Variant]

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    This will remove filter variants on affected / unaffected fractions set

  16. def finalize(): Unit

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

  17. val genotypeAnnotation: List[GenotypeAnnotation]

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  18. val genotypes: List[Genotype]

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  19. def getAffectedFractions(broadcasts: Broadcasts): Map[List[Short], Fraction]

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    Get fractions for the complete input set

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

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    Definition Classes
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  21. def getExternalFractions: Array[Map[List[Short], Option[Double]]]

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  22. def getFamilyFractions(broadcasts: Broadcasts): Array[Map[List[Short], Fraction]]

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    Returns all fractions for each family

  23. final def isInstanceOf[T0]: Boolean

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

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  25. final def notify(): Unit

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  26. final def notifyAll(): Unit

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  27. def passedFamilies(broadcasts: Broadcasts): Array[Boolean]

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    Returns a array with all families, true if they pass the fractions filters

  28. val pos: Int

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  29. val regionsIdx: Int

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

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    Definition Classes
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  31. def toCsv(broadcasts: Broadcasts): VariantCsv

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    Convert this to a csv object

  32. final def wait(): Unit

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    @throws( ... )

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

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  34. 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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