org.bdgenomics.avocado.models

Match

case class Match(size: Int, optMismatchingBases: Option[String] = None) extends ObservationOperator with Product with Serializable

An alignment match block (M), further broken down into a sequence (mis)match.

size

The size of this block.

optMismatchingBases

If this block is a sequence match (=), this will be empty. If this block is a sequence mismatch (X), this will contain the mismatching reference bases.

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

  1. new Match(size: Int, optMismatchingBases: Option[String] = None)

    size

    The size of this block.

    optMismatchingBases

    If this block is a sequence match (=), this will be empty. If this block is a sequence mismatch (X), this will contain the mismatching reference bases.

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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  7. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  9. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  10. def isSequenceMatch: Boolean

    returns

    True if there are no mismatching bases.

  11. def isSequenceMismatch: Boolean

    returns

    True if there are mismatching bases.

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

    Definition Classes
    AnyRef

  13. def nonEmpty: Boolean

    returns

    True if this block has non-zero length.

    Definition Classes
    ObservationOperator

  14. final def notify(): Unit

    Definition Classes
    AnyRef

  15. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  16. val optMismatchingBases: Option[String]

    If this block is a sequence match (=), this will be empty.

    If this block is a sequence match (=), this will be empty. If this block is a sequence mismatch (X), this will contain the mismatching reference bases.

  17. val size: Int

    The size of this block.

    The size of this block.

    Definition Classes
    Match → ObservationOperator

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

    Definition Classes
    AnyRef

  19. def toString(): String

    returns

    Returns "<length>=" if a match, "<length>X" if a mismatch.

    Definition Classes
    Match → AnyRef → Any

  20. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  22. 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 ObservationOperator

Inherited from AnyRef

Inherited from Any

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