org.hammerlab.guacamole.jointcaller.pileup_summarization

PileupStats

class PileupStats extends AnyRef

Statistics over a PileupElement instances (a pileup).

This is not a case class because we do not intend for it to be serialized, and we want to get an error if we try.

We can consider sequenced alleles of any reference length. For example, if we are evaluating support for a 10-base deletion, we want the keys returned by allelicDepths method to be the sequenced alleles aligning to that 10-base region; in particular the reference allele would be length 10. The length of the refSequence attribute establishes the reference length to be considered.

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Instance Constructors

  1. new PileupStats(elements: Seq[PileupElement], referenceSequence: Seq[Byte])

    elements

    elements from a pileup. They should all be positioned at the same locus. The alleles considered will align at this locus + 1.

    referenceSequence

    reference bases. The length determines the size of alleles to consider. The first element should be the reference base at locus elements.head.locus + 1.

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

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  6. val alleleToSubsequences: Map[String, Seq[ReadSubsequence]]

    Map from sequenced allele -> the ReadSubsequence instances for that allele.

  7. val allelicDepths: Map[String, Int]

    Map from sequenced allele -> number of reads supporting that allele.

  8. final def asInstanceOf[T0]: T0

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  9. def clone(): AnyRef

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  10. val elements: Seq[PileupElement]

    elements from a pileup.

    elements from a pileup. They should all be positioned at the same locus. The alleles considered will align at this locus + 1.

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

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  12. def equals(arg0: Any): Boolean

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  13. def finalize(): Unit

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

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  15. def hashCode(): Int

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  16. final def isInstanceOf[T0]: Boolean

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  17. def logLikelihoodPileup(mixture: AlleleMixture): Double

    Compute likelihood P(data|mixture) of the sequenced bases (data) given the specified mixture.

    Compute likelihood P(data|mixture) of the sequenced bases (data) given the specified mixture.

    Reads with mapping quality 0 are ignored.

    mixture

    Map from sequenced allele -> variant allele fraction

    returns

    log10 likelihood probability, always non-positive

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

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  19. val nonRefAlleles: Seq[String]

    All sequenced alleles that are not the ref allele, sorted by decreasing allelic depth.

  20. final def notify(): Unit

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  21. final def notifyAll(): Unit

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  22. lazy val readNamesByAllele: Map[String, Set[String]]

    Map from allele to read names supporting that allele.

  23. val ref: String

    The reference sequence as a string.

  24. val referenceSequence: Seq[Byte]

    reference bases.

    reference bases. The length determines the size of alleles to consider. The first element should be the reference base at locus elements.head.locus + 1.

  25. val secondAlt: String

    Alt allele with second-most reads.

  26. val subsequences: Seq[ReadSubsequence]

    The sequenced alleles at this site as ReadSubsequence instances.

    The sequenced alleles at this site as ReadSubsequence instances.

    Every read that is "anchored" on either side of the reference region by a matching, non-variant base is represented here.

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

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  28. def toString(): String

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  29. val topAlt: String

    Alt allele with most reads.

  30. val totalDepthIncludingReadsContributingNoAlleles: Int

    Total depth, including reads that are NOT "anchored" by matching, non-variant bases.

  31. def truncatedAllelicDepths(max: Int): Map[String, Int]

  32. def vaf(allele: String): Double

    Fraction of reads supporting the given allele.

  33. final def wait(): Unit

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

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

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