org.hammerlab.guacamole.jointcaller.pileup_summarization

ReadSubsequence

case class ReadSubsequence(read: MappedRead, startLocus: Locus, endLocus: Locus, startReadPosition: Int, endReadPosition: Int) extends Product with Serializable

A sub-sequence of the bases sequenced by a MappedRead.

read

the mapped read

startLocus

reference locus of the first base in the sub-sequence

endLocus

one past the reference locus of the last base in the sub-sequence

startReadPosition

offset into the read of the first base in the sub-sequence

endReadPosition

one past the offset into the read of last base in the sub-sequence

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Instance Constructors

  1. new ReadSubsequence(read: MappedRead, startLocus: Locus, endLocus: Locus, startReadPosition: Int, endReadPosition: Int)

    read

    the mapped read

    startLocus

    reference locus of the first base in the sub-sequence

    endLocus

    one past the reference locus of the last base in the sub-sequence

    startReadPosition

    offset into the read of the first base in the sub-sequence

    endReadPosition

    one past the offset into the read of last base in the sub-sequence

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. def baseQualities(): Seq[Int]

    The base qualities corresponding to the sequenced bases.

  8. def clone(): AnyRef

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

  9. val endLocus: Locus

    one past the reference locus of the last base in the sub-sequence

  10. val endReadPosition: Int

    one past the offset into the read of last base in the sub-sequence

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

    Definition Classes
    AnyRef

  12. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  15. def meanBaseQuality(): Double

    Average base quality of the sequenced bases.

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

    Definition Classes
    AnyRef

  17. final def notify(): Unit

    Definition Classes
    AnyRef

  18. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  19. val read: MappedRead

    the mapped read

  20. def refSequence(contigReferenceSequence: ContigSequence): String

    The reference sequence at this locus.

  21. def referenceLength: Int

    Number of reference bases spanned

  22. def sequence(): String

    The sequenced bases as a string

  23. def sequenceIsAllStandardBases(): Boolean

    true if the sequence contains only A,C,G,T (e.

    true if the sequence contains only A,C,G,T (e.g. no N's)

  24. val startLocus: Locus

    reference locus of the first base in the sub-sequence

  25. val startReadPosition: Int

    offset into the read of the first base in the sub-sequence

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

    Definition Classes
    AnyRef

  27. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  29. 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

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