ConcordanceTable

Value Members

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

   Definition Classes

   AnyRef

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

   Definition Classes

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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. def add(that: ConcordanceTable): ConcordanceTable

   Add that ConcordanceTable into this table.

   Add that ConcordanceTable into this table.

   that

   ConcordanceTable

   returns

   this

7. def add(p: (GenotypeType, GenotypeType)): ConcordanceTable

   Add single genotype-genotype comparison into this table.

   Add single genotype-genotype comparison into this table.

   p

   Tuple of (test, truth) GenotypeType

   returns

   this

8. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

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   @throws( ... )

10. def concordance: Double

    Overally genotype concordance, or the percentage of identical genotypes (including homozygous reference calls)

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

    Definition Classes

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12. def equals(arg0: Any): Boolean

    Definition Classes

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13. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

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

14. def get(test: GenotypeType, truth: GenotypeType): Long

    Get single table entry at (test, truth)

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

    Definition Classes

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16. def hashCode(): Int

    Definition Classes

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17. final def isInstanceOf[T0]: Boolean

    Definition Classes

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

    Definition Classes

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19. def nonReferenceConcordance: Double

    Non-reference concordance or NRC is similar to NRS, but requires strict zygosity matching in the numerator.

20. def nonReferenceDiscrepancy: Double

    Non-reference discrepancy is a measure of discrepant calls, excluding matching homozygous reference genotypes, which are easier to call.

21. def nonReferenceSensitivity: Double

    Non-reference sensitivity or NRS is a site-level variant sensitivity metric.

22. final def notify(): Unit

    Definition Classes

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23. final def notifyAll(): Unit

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24. def precision: Double

    Precision metric.

    Precision metric. This metric is similar to NRC but with "test" and "truth" reversed.

25. def recall: Double

    Alias for nonReferenceConcordance

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

    Definition Classes

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27. def toString(): String

    Definition Classes

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28. def total(test: EnumSet[GenotypeType], truth: EnumSet[GenotypeType]): Long

    Total of all entries indexed by the cartesian product of test and truth

29. def total(diagonal: EnumSet[GenotypeType]): Long

30. def total(): Long

31. final def wait(): Unit

    Definition Classes

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    @throws( ... )

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

    Definition Classes

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

    Definition Classes

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    @throws( ... )