Class

nl.biopet.utils.ngs.vcf

GenotypeFieldCounts

Related Doc: package vcf

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class GenotypeFieldCounts extends Serializable

This class will track all values of 1 genotype field

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Instance Constructors

  1. new GenotypeFieldCounts(header: VCFHeader, field: VCFFormatHeaderLine, method: FieldMethod.Value)

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Value Members

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

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  2. final def ##(): Int

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  3. def +=(other: GenotypeFieldCounts): GenotypeFieldCounts

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

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  5. val _noValue: Array[Long]

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    Attributes
    protected

  6. val _total: Array[Long]

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    Attributes
    protected

  7. def addRecord(record: VariantContext, sampleIdx: Option[Int] = None): Unit

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    Add records to counts

    Add records to counts

    record

    Vcf record

    sampleIdx

    Optional: Only do this given sample

  8. final def asInstanceOf[T0]: T0

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  9. def clone(): AnyRef

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    @throws( ... )

  10. val counts: Map[Int, Counts[String]]

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    Attributes
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  11. def countsMap: Map[String, Map[String, Long]]

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    Return a map of counts

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

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  13. def equals(arg0: Any): Boolean

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  14. def finalize(): Unit

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

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

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  16. def hashCode(): Int

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  17. final def isInstanceOf[T0]: Boolean

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

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  19. def noValue: Map[String, Long]

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    Returns per sample the number of records without the field

  20. final def notify(): Unit

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  21. final def notifyAll(): Unit

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  22. val samples: Map[String, Int]

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    This map binds names to sample index

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

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  24. def toString(): String

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  25. def total: Map[String, Long]

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    Returns per sample the number of total records

  26. final def wait(): Unit

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

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

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  29. def writeToFile(outputFile: File): Unit

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    Write histograms to a single file

Inherited from Serializable

Inherited from Serializable

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