HardCalls

Converts an array of probabilities (most likely the genotype probabilities from a BGEN file) into hard calls. The input probabilities are assumed to be diploid.

If the input probabilities are phased, each haplotype is called separately by finding the maximum probability greater than the threshold (0.9 by default, a la plink). If no probability is greater than the threshold, the call is -1 (missing).

If the input probabilities are unphased, the probabilities refer to the complete genotype. In this case, we find the maximum probability greater than the threshold and then convert that value to a genotype call.

If any of the required parameters (probabilities, numAlts, phased) are null, the expression returns null.

probabilities: The probabilities to convert to hard calls. The algorithm does not check that they sum to 1. If the probabilities are unphased, they are assumed to correspond to the genotypes in colex order, which is standard for both BGEN and VCF files.
numAlts: The number of alternate alleles at this site.
phased: Whether the probabilities are phased (per haplotype) or unphased (whole genotype).
threshold: Calls are only generated if at least one probability is above this threshold.

Linear Supertypes

Serializable, Serializable, ImplicitCastInputTypes, ExpectsInputTypes, CodegenFallback, Expression, TreeNode[Expression], Product, Equals, AnyRef, Any

Instance Constructors

new HardCalls(probabilities: Expression, numAlts: Expression, phased: Expression)
new HardCalls(probabilities: Expression, numAlts: Expression, phased: Expression, threshold: Expression)

probabilities
The probabilities to convert to hard calls. The algorithm does not check that they sum to 1. If the probabilities are unphased, they are assumed to correspond to the genotypes in colex order, which is standard for both BGEN and VCF files.
numAlts
The number of alternate alleles at this site.
phased
Whether the probabilities are phased (per haplotype) or unphased (whole genotype).
threshold
Calls are only generated if at least one probability is above this threshold.

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def apply(number: Int): TreeNode[_]

Definition Classes
TreeNode
def argString: String

Definition Classes
TreeNode
def asCode: String

Definition Classes
TreeNode
final def asInstanceOf[T0]: T0

Definition Classes
Any
lazy val canonicalized: Expression

Definition Classes
Expression
def checkInputDataTypes(): TypeCheckResult

Definition Classes
HardCalls → ExpectsInputTypes → Expression
def children: Seq[Expression]

Definition Classes
HardCalls → TreeNode
def childrenResolved: Boolean

Definition Classes
Expression
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def collect[B](pf: PartialFunction[Expression, B]): Seq[B]

Definition Classes
TreeNode
def collectFirst[B](pf: PartialFunction[Expression, B]): Option[B]

Definition Classes
TreeNode
def collectLeaves(): Seq[Expression]

Definition Classes
TreeNode
lazy val containsChild: Set[TreeNode[_]]

Definition Classes
TreeNode
def dataType: DataType

Definition Classes
HardCalls → Expression
lazy val deterministic: Boolean

Definition Classes
Expression
def doGenCode(ctx: CodegenContext, ev: ExprCode): ExprCode

Attributes
protected
Definition Classes
CodegenFallback → Expression
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def eval(input: InternalRow): Any

Definition Classes
HardCalls → Expression
def fastEquals(other: TreeNode[_]): Boolean

Definition Classes
TreeNode
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
def find(f: (Expression) ⇒ Boolean): Option[Expression]

Definition Classes
TreeNode
def flatArguments: Iterator[Any]

Attributes
protected
Definition Classes
Expression
def flatMap[A](f: (Expression) ⇒ TraversableOnce[A]): Seq[A]

Definition Classes
TreeNode
def foldable: Boolean

Definition Classes
Expression
def foreach(f: (Expression) ⇒ Unit): Unit

Definition Classes
TreeNode
def foreachUp(f: (Expression) ⇒ Unit): Unit

Definition Classes
TreeNode
def genCode(ctx: CodegenContext): ExprCode

Definition Classes
Expression
def generateTreeString(depth: Int, lastChildren: Seq[Boolean], builder: StringBuilder, verbose: Boolean, prefix: String, addSuffix: Boolean): StringBuilder

Definition Classes
TreeNode
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Definition Classes
TreeNode → AnyRef → Any
def innerChildren: Seq[TreeNode[_]]

Attributes
protected
Definition Classes
TreeNode
def inputTypes: Seq[Serializable with AbstractDataType]

Definition Classes
HardCalls → ExpectsInputTypes
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def jsonFields: List[JField]

Attributes
protected
Definition Classes
TreeNode
def makeCopy(newArgs: Array[AnyRef]): Expression

Definition Classes
TreeNode
def map[A](f: (Expression) ⇒ A): Seq[A]

Definition Classes
TreeNode
def mapChildren(f: (Expression) ⇒ Expression): Expression

Definition Classes
TreeNode
def mapProductIterator[B](f: (Any) ⇒ B)(implicit arg0: ClassTag[B]): Array[B]

Attributes
protected
Definition Classes
TreeNode
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def nodeName: String

Definition Classes
TreeNode
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def nullable: Boolean

Definition Classes
HardCalls → Expression
val numAlts: Expression

The number of alternate alleles at this site.
def numberedTreeString: String

Definition Classes
TreeNode
val origin: Origin

Definition Classes
TreeNode
def otherCopyArgs: Seq[AnyRef]

Attributes
protected
Definition Classes
TreeNode
def p(number: Int): Expression

Definition Classes
TreeNode
val phased: Expression

Whether the probabilities are phased (per haplotype) or unphased (whole genotype).
def prettyJson: String

Definition Classes
TreeNode
def prettyName: String

Definition Classes
Expression
val probabilities: Expression

The probabilities to convert to hard calls.
The probabilities to convert to hard calls. The algorithm does not check that they sum to 1. If the probabilities are unphased, they are assumed to correspond to the genotypes in colex order, which is standard for both BGEN and VCF files.
def references: AttributeSet

Definition Classes
Expression
lazy val resolved: Boolean

Definition Classes
Expression
def semanticEquals(other: Expression): Boolean

Definition Classes
Expression
def semanticHash(): Int

Definition Classes
Expression
def simpleString: String

Definition Classes
Expression → TreeNode
def sql: String

Definition Classes
Expression
def stringArgs: Iterator[Any]

Attributes
protected
Definition Classes
TreeNode
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val threshold: Expression

Calls are only generated if at least one probability is above this threshold.
def toJSON: String

Definition Classes
TreeNode
def toString(): String

Definition Classes
Expression → TreeNode → AnyRef → Any
def transform(rule: PartialFunction[Expression, Expression]): Expression

Definition Classes
TreeNode
def transformDown(rule: PartialFunction[Expression, Expression]): Expression

Definition Classes
TreeNode
def transformUp(rule: PartialFunction[Expression, Expression]): Expression

Definition Classes
TreeNode
def treeString(verbose: Boolean, addSuffix: Boolean): String

Definition Classes
TreeNode
def treeString: String

Definition Classes
TreeNode
final def verboseString: String

Definition Classes
Expression → TreeNode
def verboseStringWithSuffix: String

Definition Classes
TreeNode
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
def withNewChildren(newChildren: Seq[Expression]): Expression

Definition Classes
TreeNode

Related Doc: package expressions

case class HardCalls(probabilities: Expression, numAlts: Expression, phased: Expression, threshold: Expression) extends Expression with CodegenFallback with ImplicitCastInputTypes with Product with Serializable

Instance Constructors

new HardCalls(probabilities: Expression, numAlts: Expression, phased: Expression)

new HardCalls(probabilities: Expression, numAlts: Expression, phased: Expression, threshold: Expression)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def apply(number: Int): TreeNode[_]

def argString: String

def asCode: String

final def asInstanceOf[T0]: T0

lazy val canonicalized: Expression

def checkInputDataTypes(): TypeCheckResult

def children: Seq[Expression]

def childrenResolved: Boolean

def clone(): AnyRef

def collect[B](pf: PartialFunction[Expression, B]): Seq[B]

def collectFirst[B](pf: PartialFunction[Expression, B]): Option[B]

def collectLeaves(): Seq[Expression]

lazy val containsChild: Set[TreeNode[_]]

def dataType: DataType

lazy val deterministic: Boolean

def doGenCode(ctx: CodegenContext, ev: ExprCode): ExprCode

final def eq(arg0: AnyRef): Boolean

def eval(input: InternalRow): Any

def fastEquals(other: TreeNode[_]): Boolean

def finalize(): Unit

def find(f: (Expression) ⇒ Boolean): Option[Expression]

def flatArguments: Iterator[Any]

def flatMap[A](f: (Expression) ⇒ TraversableOnce[A]): Seq[A]

def foldable: Boolean

def foreach(f: (Expression) ⇒ Unit): Unit

def foreachUp(f: (Expression) ⇒ Unit): Unit

def genCode(ctx: CodegenContext): ExprCode

def generateTreeString(depth: Int, lastChildren: Seq[Boolean], builder: StringBuilder, verbose: Boolean, prefix: String, addSuffix: Boolean): StringBuilder

final def getClass(): Class[_]

def hashCode(): Int

def innerChildren: Seq[TreeNode[_]]

def inputTypes: Seq[Serializable with AbstractDataType]

final def isInstanceOf[T0]: Boolean

def jsonFields: List[JField]

def makeCopy(newArgs: Array[AnyRef]): Expression

def map[A](f: (Expression) ⇒ A): Seq[A]

def mapChildren(f: (Expression) ⇒ Expression): Expression

def mapProductIterator[B](f: (Any) ⇒ B)(implicit arg0: ClassTag[B]): Array[B]

final def ne(arg0: AnyRef): Boolean

def nodeName: String

final def notify(): Unit

final def notifyAll(): Unit

def nullable: Boolean

val numAlts: Expression

def numberedTreeString: String

val origin: Origin

def otherCopyArgs: Seq[AnyRef]

def p(number: Int): Expression

val phased: Expression

def prettyJson: String

def prettyName: String

val probabilities: Expression

def references: AttributeSet

lazy val resolved: Boolean

def semanticEquals(other: Expression): Boolean

def semanticHash(): Int

def simpleString: String

def sql: String

def stringArgs: Iterator[Any]

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

val threshold: Expression

def toJSON: String

def toString(): String

def transform(rule: PartialFunction[Expression, Expression]): Expression

def transformDown(rule: PartialFunction[Expression, Expression]): Expression

def transformUp(rule: PartialFunction[Expression, Expression]): Expression

def treeString(verbose: Boolean, addSuffix: Boolean): String

def treeString: String

final def verboseString: String

def verboseStringWithSuffix: String