org.hammerlab.guacamole.variants

Genotype

case class Genotype(alleleMixture: Map[Allele, Double]) extends Product with Serializable

A Genotype is a map of alleles to their allele frequency

A Genotype is for a particular reference locus. Each allele gives the base(s) present on a chromosome at that locus.

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Instance Constructors

  1. new Genotype(alleleMixture: Map[Allele, Double])

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. val alleleMixture: Map[Allele, Double]

  7. val alleles: Set[Allele]

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. lazy val getNonReferenceAlleles: Set[Allele]

  14. lazy val hasVariantAllele: Boolean

    Returns whether this genotype contains any non-reference alleles for a given reference sequence.

    Returns whether this genotype contains any non-reference alleles for a given reference sequence.

    returns

    True if at least one allele is not the reference

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  17. final def notify(): Unit

    Definition Classes
    AnyRef

  18. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  19. lazy val numberOfVariantAlleles: Int

    Counts alleles in this genotype that are not the same as the specified reference allele.

    Counts alleles in this genotype that are not the same as the specified reference allele.

    returns

    Count of non reference alleles

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

    Definition Classes
    AnyRef

  21. def toString(): String

    Definition Classes
    Genotype → AnyRef → Any

  22. final def wait(): Unit

    Definition Classes
    AnyRef
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

    Definition Classes
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Inherited from Serializable

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Inherited from AnyRef

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