org.hammerlab.guacamole.alignment

ReadAlignment

case class ReadAlignment(alignments: Seq[AlignmentState], refStartIdx: Int, refEndIdx: Int, alignmentScore: Int) extends Product with Serializable

alignments

Sequence of alignments

refStartIdx

Start of the alignment in the reference sequence

refEndIdx

End of the alignment (inclusive) in the reference sequence

alignmentScore

Score of the alignment based on the mismatch and gap penalties

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Serializable, Serializable, Product, Equals, AnyRef, Any
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Instance Constructors

  1. new ReadAlignment(alignments: Seq[AlignmentState], refStartIdx: Int, refEndIdx: Int, alignmentScore: Int)

    alignments

    Sequence of alignments

    refStartIdx

    Start of the alignment in the reference sequence

    refEndIdx

    End of the alignment (inclusive) in the reference sequence

    alignmentScore

    Score of the alignment based on the mismatch and gap penalties

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 alignmentScore: Int

    Score of the alignment based on the mismatch and gap penalties

  7. val alignments: Seq[AlignmentState]

    Sequence of alignments

  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
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    @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 refEndIdx: Int

    End of the alignment (inclusive) in the reference sequence

  18. val refStartIdx: Int

    Start of the alignment in the reference sequence

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

    Definition Classes
    AnyRef

  20. def toCigar: Cigar

  21. def toCigarString: String

    Convert a ReadAlignment to a CIGAR string

    Convert a ReadAlignment to a CIGAR string

    returns

    CIGAR String

  22. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @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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    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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