Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

   AnyRef → Any

3.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

4.  def arraySummaryStats(arrayData: ArrayData): InternalRow

   Calculates basic summary stats (min, max, mean, sample stddev) on an array of double typed values.

   Calculates basic summary stats (min, max, mean, sample stddev) on an array of double typed values. These are calculated using a one pass algorithm described in https://arxiv.org/abs/1510.04923

   The algorithm used is adapted from org.apache.spark.sql.catalyst.expressions.aggregate.CentralMomentAgg

5.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

6.  def callStats(genotypes: ArrayData, genotypesSize: Int, genotypeIdx: Int): InternalRow
7.  def callStatsBase(genotypes: ArrayData, genotypesSize: Int, genotypesIdx: Int): CallStatsStruct

   Calculates a variety of summary stats on the calls for a given site.

   Calculates a variety of summary stats on the calls for a given site. This method returns a case class so that the output can be used easily from other QC functions as well as returned directly to the user.

   genotypes

   an array of structs with the schema defined in CallStats.requiredSchema

   genotypesIdx

   the position of the calls within the element struct of the genotypes array

8.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @native() @throws( ... )

9.  final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

10.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

11.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

12.  final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

    Annotations

    @native()

13.  def hardyWeinberg(genotypes: ArrayData, genotypesSize: Int, genotypeIdx: Int): GenericInternalRow

    Performs a two-sided test of the Hardy-Weinberg equilibrium.

    Performs a two-sided test of the Hardy-Weinberg equilibrium. Returns the expected het frequency as well as the associated p value.

    genotypes

    an array of structs with the schema required by CallStats

    genotypeIdx

    the position of the genotype struct (with calls and phasing info) within the element struct of the genotypes array

    returns

    a row with the schema of HardyWeinbergStruct

14.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

    Annotations

    @native()

15.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

16.  lazy val logger: Logger

    Attributes

    protected

    Definition Classes

    LazyLogging

17.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

18.  final def notify(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

19.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

20.  def subsetExpr(schema: StructType, expr: Expression): Expression

    Converts an array of struct-typed expressions into a slimmed down struct with a subset of the fields.

    Converts an array of struct-typed expressions into a slimmed down struct with a subset of the fields.

    We use this function for many of the variant QC functions so that each function can require a specific schema without requiring that the VCFRow schema remain fixed for all time.

    schema

    the desired schema

    expr

    an array of struct-typed expressions that contains a superset of the fields in schema

    returns

    a transformed array of struct-typed expressions with the schema of schema

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

    Definition Classes

    AnyRef

22.  def toString(): String

    Definition Classes

    AnyRef → Any

23.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

25.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @native() @throws( ... )