Packages

case class RichAlignment(record: Alignment) extends Product with Serializable

An enriched version of an Avro Alignment.

record

The underlying read.

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Serializable, Serializable, Product, Equals, AnyRef, Any
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  1. RichAlignment
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Instance Constructors

  1. new RichAlignment(record: Alignment)

    record

    The underlying read.

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[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def fivePrimePosition: Long

    returns

    The position of the five prime end of the read.

  8. def fivePrimeReferencePosition: ReferencePosition

    returns

    The position of the five prime end of the read, wrapped as a reference position.

  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  10. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  11. def isMismatchAtReferencePosition(pos: ReferencePosition): Option[Boolean]

    pos

    The reference position to check for a mismatch.

    returns

    Returns true if this read overlaps the given reference position, and the base aligned at this position is a mismatch against the reference genome..

  12. lazy val mdTag: Option[MdTag]

    The MdTag if the read is mapped, None otherwise

  13. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  15. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  16. def overlapsReferencePosition(pos: ReferencePosition): Boolean

    pos

    The reference position to check for overlap.

    returns

    Returns true if this read overlaps the given reference position.

  17. lazy val qualityScoreValues: Array[Int]

    The quality scores as a list of integers.

    The quality scores as a list of integers. Assumes Illumina (33) encoding.

  18. val record: Alignment
  19. lazy val samtoolsCigar: Cigar

    Parses the text CIGAR representation of the alignment.

  20. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  21. lazy val tags: Seq[Attribute]

    On access, parses the attribute tags ("key:type:value" triples) into usable records.

  22. lazy val unclippedEnd: Long

    The position of the unclipped end if the read is mapped, None otherwise.

    The position of the unclipped end if the read is mapped, None otherwise.

    Note

    The unclipped position assumes that any clipped bases would've been aligned as an alignment match.

  23. lazy val unclippedStart: Long

    The position of the unclipped start if the read is mapped, None otherwise.

    The position of the unclipped start if the read is mapped, None otherwise.

    Note

    The unclipped position assumes that any clipped bases would've been aligned as an alignment match.

  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( ... ) @native()
  26. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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