org.hammerlab.guacamole.pileup

Deletion

case class Deletion(referenceBases: Seq[Byte], baseQuality: Byte) extends Alignment with Product with Serializable

For now, only emit a Deletion at the position immediately preceding the run of deleted bases, i.e. the position we would ultimately emit a variant at (by VCF convention).

For reads at loci in the middle of a deletion, emit MidDeletion below.

Deletion stores the reference bases of the entire deletion, including the base immediately before the deletion.

referenceBases

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

  1. new Deletion(referenceBases: Seq[Byte], baseQuality: Byte)

    referenceBases

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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. val baseQuality: Byte

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def equals(other: Any): Boolean

    Definition Classes
    Deletion → Equals → AnyRef → Any

  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. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  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. val referenceBases: Seq[Byte]

    Definition Classes
    Deletion → Alignment

  18. val sequencedBases: Seq[Byte]

    Definition Classes
    Deletion → Alignment

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

    Definition Classes
    AnyRef

  20. def toString(): String

    Definition Classes
    Alignment → AnyRef → Any

  21. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  23. 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 Alignment

Inherited from AnyRef

Inherited from Any

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