c

io.projectglow.sql.expressions

CallSummaryStats

case class CallSummaryStats(genotypes: Expression, refAllele: Expression, altAlleles: Expression, mutableAggBufferOffset: Int, inputAggBufferOffset: Int) extends TypedImperativeAggregate[ArrayBuffer[SampleCallStats]] with ExpectsGenotypeFields with GlowLogging with Product with Serializable

Computes summary statistics per-sample in a genomic cohort. These statistics include the call rate and the number of different types of variants.

The return type is an array of summary statistics. If sample ids are included in the input schema, they'll be propagated to the results.

Linear Supertypes
Serializable, Serializable, GlowLogging, LazyLogging, ExpectsGenotypeFields, TypedImperativeAggregate[ArrayBuffer[SampleCallStats]], ImperativeAggregate, CodegenFallback, AggregateFunction, Expression, TreeNode[Expression], Product, Equals, AnyRef, Any
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Inherited
  1. CallSummaryStats
  2. Serializable
  3. Serializable
  4. GlowLogging
  5. LazyLogging
  6. ExpectsGenotypeFields
  7. TypedImperativeAggregate
  8. ImperativeAggregate
  9. CodegenFallback
  10. AggregateFunction
  11. Expression
  12. TreeNode
  13. Product
  14. Equals
  15. AnyRef
  16. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new CallSummaryStats(genotypes: Expression, refAllele: Expression, altAlleles: Expression)
  2. new CallSummaryStats(genotypes: Expression, refAllele: Expression, altAlleles: Expression, mutableAggBufferOffset: Int, inputAggBufferOffset: Int)

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. final lazy val aggBufferAttributes: Seq[AttributeReference]
    Definition Classes
    TypedImperativeAggregate → AggregateFunction
  5. final def aggBufferSchema: StructType
    Definition Classes
    TypedImperativeAggregate → AggregateFunction
  6. val altAlleles: Expression
  7. def apply(number: Int): TreeNode[_]
    Definition Classes
    TreeNode
  8. def argString: String
    Definition Classes
    TreeNode
  9. def asCode: String
    Definition Classes
    TreeNode
  10. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  11. lazy val canonicalized: Expression
    Definition Classes
    Expression
  12. def checkInputDataTypes(): TypeCheckResult
    Definition Classes
    CallSummaryStats → ExpectsGenotypeFields → Expression
  13. def children: Seq[Expression]
    Definition Classes
    CallSummaryStats → TreeNode
  14. def childrenResolved: Boolean
    Definition Classes
    Expression
  15. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  16. def collect[B](pf: PartialFunction[Expression, B]): Seq[B]
    Definition Classes
    TreeNode
  17. def collectFirst[B](pf: PartialFunction[Expression, B]): Option[B]
    Definition Classes
    TreeNode
  18. def collectLeaves(): Seq[Expression]
    Definition Classes
    TreeNode
  19. lazy val containsChild: Set[TreeNode[_]]
    Definition Classes
    TreeNode
  20. def createAggregationBuffer(): ArrayBuffer[SampleCallStats]
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  21. def dataType: DataType
    Definition Classes
    CallSummaryStats → Expression
  22. def defaultResult: Option[Literal]
    Definition Classes
    AggregateFunction
  23. def deserialize(storageFormat: Array[Byte]): ArrayBuffer[SampleCallStats]
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  24. lazy val deterministic: Boolean
    Definition Classes
    Expression
  25. def doGenCode(ctx: CodegenContext, ev: ExprCode): ExprCode
    Attributes
    protected
    Definition Classes
    CodegenFallback → Expression
  26. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. def eval(buffer: ArrayBuffer[SampleCallStats]): Any
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  28. final def eval(buffer: InternalRow): Any
    Definition Classes
    TypedImperativeAggregate → Expression
  29. def fastEquals(other: TreeNode[_]): Boolean
    Definition Classes
    TreeNode
  30. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  31. def find(f: (Expression) ⇒ Boolean): Option[Expression]
    Definition Classes
    TreeNode
  32. def flatArguments: Iterator[Any]
    Attributes
    protected
    Definition Classes
    Expression
  33. def flatMap[A](f: (Expression) ⇒ TraversableOnce[A]): Seq[A]
    Definition Classes
    TreeNode
  34. final def foldable: Boolean
    Definition Classes
    AggregateFunction → Expression
  35. def foreach(f: (Expression) ⇒ Unit): Unit
    Definition Classes
    TreeNode
  36. def foreachUp(f: (Expression) ⇒ Unit): Unit
    Definition Classes
    TreeNode
  37. def genCode(ctx: CodegenContext): ExprCode
    Definition Classes
    Expression
  38. def generateTreeString(depth: Int, lastChildren: Seq[Boolean], builder: StringBuilder, verbose: Boolean, prefix: String, addSuffix: Boolean): StringBuilder
    Definition Classes
    TreeNode
  39. lazy val genotypeFieldIndices: Seq[Int]
    Attributes
    protected
    Definition Classes
    ExpectsGenotypeFields
  40. def genotypeFieldsRequired: Seq[StructField]
    Definition Classes
    CallSummaryStats → ExpectsGenotypeFields
  41. lazy val genotypeStructSize: Int
    Attributes
    protected
    Definition Classes
    ExpectsGenotypeFields
  42. val genotypes: Expression
  43. def genotypesExpr: Expression
    Definition Classes
    CallSummaryStats → ExpectsGenotypeFields
  44. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  45. def hashCode(): Int
    Definition Classes
    TreeNode → AnyRef → Any
  46. final def initialize(buffer: InternalRow): Unit
    Definition Classes
    TypedImperativeAggregate → ImperativeAggregate
  47. def innerChildren: Seq[TreeNode[_]]
    Attributes
    protected
    Definition Classes
    TreeNode
  48. final lazy val inputAggBufferAttributes: Seq[AttributeReference]
    Definition Classes
    TypedImperativeAggregate → AggregateFunction
  49. val inputAggBufferOffset: Int
    Definition Classes
    CallSummaryStats → ImperativeAggregate
  50. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  51. def jsonFields: List[JField]
    Attributes
    protected
    Definition Classes
    TreeNode
  52. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  53. def makeCopy(newArgs: Array[AnyRef]): Expression
    Definition Classes
    TreeNode
  54. def map[A](f: (Expression) ⇒ A): Seq[A]
    Definition Classes
    TreeNode
  55. def mapChildren(f: (Expression) ⇒ Expression): Expression
    Definition Classes
    TreeNode
  56. def mapProductIterator[B](f: (Any) ⇒ B)(implicit arg0: ClassTag[B]): Array[B]
    Attributes
    protected
    Definition Classes
    TreeNode
  57. def merge(buffer: ArrayBuffer[SampleCallStats], input: ArrayBuffer[SampleCallStats]): ArrayBuffer[SampleCallStats]
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  58. final def merge(buffer: InternalRow, inputBuffer: InternalRow): Unit
    Definition Classes
    TypedImperativeAggregate → ImperativeAggregate
  59. val mutableAggBufferOffset: Int
    Definition Classes
    CallSummaryStats → ImperativeAggregate
  60. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  61. def nodeName: String
    Definition Classes
    TreeNode
  62. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  63. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  64. def nullable: Boolean
    Definition Classes
    CallSummaryStats → Expression
  65. def numberedTreeString: String
    Definition Classes
    TreeNode
  66. lazy val optionalFieldIndices: Seq[Int]
    Attributes
    protected
    Definition Classes
    ExpectsGenotypeFields
  67. def optionalGenotypeFields: Seq[StructField]
    Definition Classes
    CallSummaryStats → ExpectsGenotypeFields
  68. val origin: Origin
    Definition Classes
    TreeNode
  69. def otherCopyArgs: Seq[AnyRef]
    Attributes
    protected
    Definition Classes
    TreeNode
  70. def p(number: Int): Expression
    Definition Classes
    TreeNode
  71. def prettyJson: String
    Definition Classes
    TreeNode
  72. def prettyName: String
    Definition Classes
    Expression
  73. val refAllele: Expression
  74. def references: AttributeSet
    Definition Classes
    Expression
  75. lazy val resolved: Boolean
    Definition Classes
    Expression
  76. def semanticEquals(other: Expression): Boolean
    Definition Classes
    Expression
  77. def semanticHash(): Int
    Definition Classes
    Expression
  78. def serialize(buffer: ArrayBuffer[SampleCallStats]): Array[Byte]
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  79. final def serializeAggregateBufferInPlace(buffer: InternalRow): Unit
    Definition Classes
    TypedImperativeAggregate
  80. def simpleString: String
    Definition Classes
    Expression → TreeNode
  81. def sql(isDistinct: Boolean): String
    Definition Classes
    AggregateFunction
  82. def sql: String
    Definition Classes
    Expression
  83. def stringArgs: Iterator[Any]
    Attributes
    protected
    Definition Classes
    TreeNode
  84. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  85. def toAggString(isDistinct: Boolean): String
    Definition Classes
    AggregateFunction
  86. def toAggregateExpression(isDistinct: Boolean): AggregateExpression
    Definition Classes
    AggregateFunction
  87. def toAggregateExpression(): AggregateExpression
    Definition Classes
    AggregateFunction
  88. def toJSON: String
    Definition Classes
    TreeNode
  89. def toString(): String
    Definition Classes
    Expression → TreeNode → AnyRef → Any
  90. def transform(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  91. def transformDown(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  92. def transformUp(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  93. def treeString(verbose: Boolean, addSuffix: Boolean): String
    Definition Classes
    TreeNode
  94. def treeString: String
    Definition Classes
    TreeNode
  95. def update(buffer: ArrayBuffer[SampleCallStats], input: InternalRow): ArrayBuffer[SampleCallStats]
    Definition Classes
    CallSummaryStats → TypedImperativeAggregate
  96. final def update(buffer: InternalRow, input: InternalRow): Unit
    Definition Classes
    TypedImperativeAggregate → ImperativeAggregate
  97. final def verboseString: String
    Definition Classes
    Expression → TreeNode
  98. def verboseStringWithSuffix: String
    Definition Classes
    TreeNode
  99. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  100. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  101. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  102. def withNewChildren(newChildren: Seq[Expression]): Expression
    Definition Classes
    TreeNode
  103. def withNewInputAggBufferOffset(newInputAggBufferOffset: Int): ImperativeAggregate
    Definition Classes
    CallSummaryStats → ImperativeAggregate
  104. def withNewMutableAggBufferOffset(newOffset: Int): ImperativeAggregate
    Definition Classes
    CallSummaryStats → ImperativeAggregate

Inherited from Serializable

Inherited from Serializable

Inherited from GlowLogging

Inherited from LazyLogging

Inherited from ExpectsGenotypeFields

Inherited from TypedImperativeAggregate[ArrayBuffer[SampleCallStats]]

Inherited from ImperativeAggregate

Inherited from CodegenFallback

Inherited from AggregateFunction

Inherited from Expression

Inherited from TreeNode[Expression]

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped