org.bdgenomics.avocado.models

Observation

case class Observation(alleleForwardStrand: Int, otherForwardStrand: Int, squareMapQ: Double, referenceLogLikelihoods: Array[Double], alleleLogLikelihoods: Array[Double], otherLogLikelihoods: Array[Double], nonRefLogLikelihoods: Array[Double], alleleCoverage: Int, otherCoverage: Int, totalCoverage: Int, isRef: Boolean, copyNumber: Int) extends Product with Serializable

A generic class that stores likelihoods and simple annotations.

alleleForwardStrand

The number of reads covering the allele observed on the forward strand.

otherForwardStrand

The number of reads covering the site but not matching the allele observed on the forward strand.

squareMapQ

The sum of the squares of the mapping qualities observed.

referenceLogLikelihoods

The log likelihoods that 0...n copies of the reference allele were observed.

alleleLogLikelihoods

The log likelihoods that 0...n copies of this allele were observed.

otherLogLikelihoods

The log likelihoods that 0...n copies of an unknown allele were observed.

alleleCoverage

The total number of reads observed that cover the site and match the allele.

otherCoverage

The total number of reads observed that cover the site but that do not match the allele.

totalCoverage

The total number of reads that cover the site.

isRef

True if this allele matches the reference.

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

  1. new Observation(alleleForwardStrand: Int, otherForwardStrand: Int, squareMapQ: Double, referenceLogLikelihoods: Array[Double], alleleLogLikelihoods: Array[Double], otherLogLikelihoods: Array[Double], nonRefLogLikelihoods: Array[Double], alleleCoverage: Int, otherCoverage: Int, totalCoverage: Int, isRef: Boolean, copyNumber: Int)

    alleleForwardStrand

    The number of reads covering the allele observed on the forward strand.

    otherForwardStrand

    The number of reads covering the site but not matching the allele observed on the forward strand.

    squareMapQ

    The sum of the squares of the mapping qualities observed.

    referenceLogLikelihoods

    The log likelihoods that 0...n copies of the reference allele were observed.

    alleleLogLikelihoods

    The log likelihoods that 0...n copies of this allele were observed.

    otherLogLikelihoods

    The log likelihoods that 0...n copies of an unknown allele were observed.

    alleleCoverage

    The total number of reads observed that cover the site and match the allele.

    otherCoverage

    The total number of reads observed that cover the site but that do not match the allele.

    totalCoverage

    The total number of reads that cover the site.

    isRef

    True if this allele matches the reference.

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 alleleCoverage: Int

    The total number of reads observed that cover the site and match the allele.

  7. val alleleForwardStrand: Int

    The number of reads covering the allele observed on the forward strand.

  8. val alleleLogLikelihoods: Array[Double]

    The log likelihoods that 0.

    The log likelihoods that 0...n copies of this allele were observed.

  9. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  10. def clone(): AnyRef

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

  11. val copyNumber: Int

  12. def coverage: Int

    returns

    The total coverage of this site.

  13. def duplicate(setRef: Option[Boolean] = None): Observation

    returns

    Makes a copy where underlying arrays are not shared.

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

    Definition Classes
    AnyRef

  15. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  17. def invert: Observation

    returns

    Returns this observation, but with allele/other swapped.

    See also

    null

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  19. val isRef: Boolean

    True if this allele matches the reference.

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

    Definition Classes
    AnyRef

  21. val nonRefLogLikelihoods: Array[Double]

  22. final def notify(): Unit

    Definition Classes
    AnyRef

  23. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  24. def nullOut: Observation

    returns

    Returns this observation, but with all allele related fields nulled out.

    See also

    invert

  25. val otherCoverage: Int

    The total number of reads observed that cover the site but that do not match the allele.

  26. val otherForwardStrand: Int

    The number of reads covering the site but not matching the allele observed on the forward strand.

  27. val otherLogLikelihoods: Array[Double]

    The log likelihoods that 0.

    The log likelihoods that 0...n copies of an unknown allele were observed.

  28. val referenceLogLikelihoods: Array[Double]

    The log likelihoods that 0.

    The log likelihoods that 0...n copies of the reference allele were observed.

  29. val squareMapQ: Double

    The sum of the squares of the mapping qualities observed.

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

    Definition Classes
    AnyRef

  31. def toString(): String

    Definition Classes
    Observation → AnyRef → Any

  32. val totalCoverage: Int

    The total number of reads that cover the site.

  33. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  35. 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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