org.hammerlab.guacamole.pileup

Pileup

case class Pileup(sampleName: SampleName, contigName: ContigName, locus: Locus, contigSequence: ContigSequence, elements: Seq[PileupElement]) extends Product with Serializable

A Pileup at a locus contains a sequence of PileupElement instances, one for every read that overlaps that locus. Each PileupElement specifies the base read at the given locus in a particular read. It also keeps track of the read itself and the offset of the base in the read.

contigName

The contig name for all elements in this pileup.

locus

The locus on the reference genome

contigSequence

The reference for this contig

elements

Sequence of PileupElement instances giving the sequenced bases that align to a particular reference locus, in arbitrary order.

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Instance Constructors

  1. new Pileup(sampleName: SampleName, contigName: ContigName, locus: Locus, contigSequence: ContigSequence, elements: Seq[PileupElement])

    contigName

    The contig name for all elements in this pileup.

    locus

    The locus on the reference genome

    contigSequence

    The reference for this contig

    elements

    Sequence of PileupElement instances giving the sequenced bases that align to a particular reference locus, in arbitrary order.

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. def alleleReadDepthAndPositiveDepth(allele: Allele): (Int, Int)

    Compute depth and positive strand depth of a particular alternate base

    Compute depth and positive strand depth of a particular alternate base

    allele

    allele to consider

    returns

    tuple of total depth and forward strand depth

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def atGreaterLocus(newLocus: Locus, newReads: Iterator[MappedRead]): Pileup

    Returns a new Pileup at a different locus on the same contig.

    Returns a new Pileup at a different locus on the same contig.

    To enable an efficient implementation, the new locus must be greater than the current locus.

    newLocus

    The locus to move forward to.

    newReads

    The *new* reads, i.e. those that overlap the new locus, but not the current locus.

    returns

    A new Pileup at the given locus.

  9. def clone(): AnyRef

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

  10. val contigName: ContigName

    The contig name for all elements in this pileup.

  11. val contigSequence: ContigSequence

    The reference for this contig

  12. lazy val depth: Int

    Depth of pileup - number of reads at locus

  13. lazy val distinctAlleles: Seq[Allele]

  14. val elements: Seq[PileupElement]

    Sequence of PileupElement instances giving the sequenced bases that align to a particular reference locus, in arbitrary order.

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

    Definition Classes
    AnyRef

  16. def finalize(): Unit

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

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

    Definition Classes
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  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
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  19. val locus: Locus

    The locus on the reference genome

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

    Definition Classes
    AnyRef

  21. final def notify(): Unit

    Definition Classes
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  22. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  23. lazy val positiveDepth: Int

    Number of positively stranded reads

  24. val referenceBase: Byte

  25. lazy val referenceDepth: Int

    PileupElements that match the reference base

  26. lazy val referenceElements: Seq[PileupElement]

    PileupElements that match the reference base

  27. val sampleName: SampleName

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

    Definition Classes
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  29. final def wait(): Unit

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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

  31. final def wait(arg0: Long): Unit

    Definition Classes
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    @throws( ... )

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