org.hammerlab.guacamole.variants

AlleleEvidence

case class AlleleEvidence(likelihood: Double, readDepth: Int, alleleReadDepth: Int, forwardDepth: Int, alleleForwardDepth: Int, meanMappingQuality: Double, medianMappingQuality: Double, meanBaseQuality: Double, medianBaseQuality: Double, medianMismatchesPerRead: Double) extends Product with Serializable

Sample specific pileup and read statistics in support of a given variant

likelihood

probability of the genotype

readDepth

total reads at the genotype position

alleleReadDepth

total reads with allele base at the genotype position

forwardDepth

total reads on the forward strand at the genotype position

alleleForwardDepth

total reads with allele base on the forward strand at the genotype position

meanMappingQuality

mean mapping quality of reads

medianMappingQuality

median mapping quality of reads

meanBaseQuality

mean base quality of bases covering this position

medianBaseQuality

median base quality of bases covering this position

medianMismatchesPerRead

median number of mismatches on reads supporting this variant

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Instance Constructors

  1. new AlleleEvidence(likelihood: Double, readDepth: Int, alleleReadDepth: Int, forwardDepth: Int, alleleForwardDepth: Int, meanMappingQuality: Double, medianMappingQuality: Double, meanBaseQuality: Double, medianBaseQuality: Double, medianMismatchesPerRead: Double)

    likelihood

    probability of the genotype

    readDepth

    total reads at the genotype position

    alleleReadDepth

    total reads with allele base at the genotype position

    forwardDepth

    total reads on the forward strand at the genotype position

    alleleForwardDepth

    total reads with allele base on the forward strand at the genotype position

    meanMappingQuality

    mean mapping quality of reads

    medianMappingQuality

    median mapping quality of reads

    meanBaseQuality

    mean base quality of bases covering this position

    medianBaseQuality

    median base quality of bases covering this position

    medianMismatchesPerRead

    median number of mismatches on reads supporting this variant

Value Members

  1. final def !=(arg0: AnyRef): Boolean

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  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

    Definition Classes
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  6. val alleleForwardDepth: Int

    total reads with allele base on the forward strand at the genotype position

  7. val alleleReadDepth: Int

    total reads with allele base at the genotype position

  8. final def asInstanceOf[T0]: T0

    Definition Classes
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  9. def clone(): AnyRef

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    protected[java.lang]
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  10. final def eq(arg0: AnyRef): Boolean

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  11. def finalize(): Unit

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    @throws( classOf[java.lang.Throwable] )

  12. val forwardDepth: Int

    total reads on the forward strand at the genotype position

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

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

    Definition Classes
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  15. val likelihood: Double

    probability of the genotype

  16. val meanBaseQuality: Double

    mean base quality of bases covering this position

  17. val meanMappingQuality: Double

    mean mapping quality of reads

  18. val medianBaseQuality: Double

    median base quality of bases covering this position

  19. val medianMappingQuality: Double

    median mapping quality of reads

  20. val medianMismatchesPerRead: Double

    median number of mismatches on reads supporting this variant

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

    Definition Classes
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  22. final def notify(): Unit

    Definition Classes
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  23. final def notifyAll(): Unit

    Definition Classes
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  24. lazy val phredScaledLikelihood: Int

  25. val readDepth: Int

    total reads at the genotype position

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

    Definition Classes
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  27. lazy val variantAlleleFrequency: Float

  28. final def wait(): Unit

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

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

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