org.bdgenomics.avocado.genotyping

DiscoveredVariant

case class DiscoveredVariant(contigName: String, start: Int, referenceAllele: String, alternateAllele: Option[String]) extends Product with Serializable

A variant site and alleles.

contigName

The contig this variant is on.

start

The position this variant starts at.

referenceAllele

The reference allele this variant varies from.

alternateAllele

The substituted allele.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. DiscoveredVariant
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. AnyRef
  7. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new DiscoveredVariant(contigName: String, start: Int, referenceAllele: String, alternateAllele: Option[String])

    contigName

    The contig this variant is on.

    start

    The position this variant starts at.

    referenceAllele

    The reference allele this variant varies from.

    alternateAllele

    The substituted allele.

Value Members

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

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef → Any

  4. val alternateAllele: Option[String]

    The substituted allele.

  5. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  6. def clone(): AnyRef

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

  7. val contigName: String

    The contig this variant is on.

  8. lazy val end: Int

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

    Definition Classes
    AnyRef

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  13. def isNonRefModel: Boolean

    returns

    True if this is a symbolic model of a non-ref allele.

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

    Definition Classes
    AnyRef

  15. final def notify(): Unit

    Definition Classes
    AnyRef

  16. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  17. def overlaps(rr: ReferenceRegion): Boolean

  18. def overlaps(v: DiscoveredVariant): Boolean

  19. val referenceAllele: String

    The reference allele this variant varies from.

  20. val start: Int

    The position this variant starts at.

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

    Definition Classes
    AnyRef

  22. def toVariant: Variant

    returns

    Returns an avro representation of this variant.

  23. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped