c

io.projectglow.sql.expressions

LiftOverCoordinatesExpr

case class LiftOverCoordinatesExpr(contigName: Expression, start: Expression, end: Expression, chainFile: Expression, minMatchRatio: Expression) extends Expression with CodegenFallback with ImplicitCastInputTypes with Product with Serializable

Performs lift over from the specified 0-start, half-open interval (contigName, start, end) on the reference sequence to a query sequence, using the specified chain file and minimum fraction of bases that must remap.

We assume the chain file is a constant value so that the LiftOver object can be reused between rows.

If any of the required parameters (contigName, start, end) are null, the expression returns null. If minMatchRatioOpt contains null, the expression returns null; if it is empty, we use 0.95 to match LiftOver.DEFAULT_LIFTOVER_MINMATCH.

contigName

Chromosome name on the reference sequence.

start

Start position (0-start) on the reference sequence.

end

End position on the reference sequence.

chainFile

UCSC chain format file mapping blocks from the reference sequence to the query sequence.

minMatchRatio

The minimum fraction of bases that must remap to lift over successfully.

Linear Supertypes
Serializable, Serializable, ImplicitCastInputTypes, ExpectsInputTypes, CodegenFallback, Expression, TreeNode[Expression], Product, Equals, AnyRef, Any
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Inherited
  1. LiftOverCoordinatesExpr
  2. Serializable
  3. Serializable
  4. ImplicitCastInputTypes
  5. ExpectsInputTypes
  6. CodegenFallback
  7. Expression
  8. TreeNode
  9. Product
  10. Equals
  11. AnyRef
  12. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new LiftOverCoordinatesExpr(contigName: Expression, start: Expression, end: Expression, chainFile: Expression)
  2. new LiftOverCoordinatesExpr(contigName: Expression, start: Expression, end: Expression, chainFile: Expression, minMatchRatio: Expression)

    contigName

    Chromosome name on the reference sequence.

    start

    Start position (0-start) on the reference sequence.

    end

    End position on the reference sequence.

    chainFile

    UCSC chain format file mapping blocks from the reference sequence to the query sequence.

    minMatchRatio

    The minimum fraction of bases that must remap to lift over successfully.

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 apply(number: Int): TreeNode[_]
    Definition Classes
    TreeNode
  5. def argString: String
    Definition Classes
    TreeNode
  6. def asCode: String
    Definition Classes
    TreeNode
  7. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  8. lazy val canonicalized: Expression
    Definition Classes
    Expression
  9. val chainFile: Expression
  10. def checkInputDataTypes(): TypeCheckResult
    Definition Classes
    LiftOverCoordinatesExpr → ExpectsInputTypes → Expression
  11. def children: Seq[Expression]
    Definition Classes
    LiftOverCoordinatesExpr → TreeNode
  12. def childrenResolved: Boolean
    Definition Classes
    Expression
  13. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  14. def collect[B](pf: PartialFunction[Expression, B]): Seq[B]
    Definition Classes
    TreeNode
  15. def collectFirst[B](pf: PartialFunction[Expression, B]): Option[B]
    Definition Classes
    TreeNode
  16. def collectLeaves(): Seq[Expression]
    Definition Classes
    TreeNode
  17. lazy val containsChild: Set[TreeNode[_]]
    Definition Classes
    TreeNode
  18. val contigName: Expression
  19. def dataType: DataType
    Definition Classes
    LiftOverCoordinatesExpr → Expression
  20. lazy val deterministic: Boolean
    Definition Classes
    Expression
  21. def doGenCode(ctx: CodegenContext, ev: ExprCode): ExprCode
    Attributes
    protected
    Definition Classes
    CodegenFallback → Expression
  22. val end: Expression
  23. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. def eval(input: InternalRow): Any

    Performs lift over from the input row.

    Performs lift over from the input row. The LiftOver API uses a 1-start, fully-closed interval.

    input

    A row containing a 0-start, half-open interval on the reference sequence.

    returns

    A struct containing a 0-start, half-open interval (contigName, start, end) on the query sequence.

    Definition Classes
    LiftOverCoordinatesExpr → Expression
  25. def fastEquals(other: TreeNode[_]): Boolean
    Definition Classes
    TreeNode
  26. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  27. def find(f: (Expression) ⇒ Boolean): Option[Expression]
    Definition Classes
    TreeNode
  28. def flatArguments: Iterator[Any]
    Attributes
    protected
    Definition Classes
    Expression
  29. def flatMap[A](f: (Expression) ⇒ TraversableOnce[A]): Seq[A]
    Definition Classes
    TreeNode
  30. def foldable: Boolean
    Definition Classes
    Expression
  31. def foreach(f: (Expression) ⇒ Unit): Unit
    Definition Classes
    TreeNode
  32. def foreachUp(f: (Expression) ⇒ Unit): Unit
    Definition Classes
    TreeNode
  33. def genCode(ctx: CodegenContext): ExprCode
    Definition Classes
    Expression
  34. def generateTreeString(depth: Int, lastChildren: Seq[Boolean], builder: StringBuilder, verbose: Boolean, prefix: String, addSuffix: Boolean): StringBuilder
    Definition Classes
    TreeNode
  35. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  36. def hashCode(): Int
    Definition Classes
    TreeNode → AnyRef → Any
  37. def innerChildren: Seq[TreeNode[_]]
    Attributes
    protected
    Definition Classes
    TreeNode
  38. def inputTypes: Seq[Serializable with AbstractDataType]
    Definition Classes
    LiftOverCoordinatesExpr → ExpectsInputTypes
  39. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  40. def jsonFields: List[JField]
    Attributes
    protected
    Definition Classes
    TreeNode
  41. def makeCopy(newArgs: Array[AnyRef]): Expression
    Definition Classes
    TreeNode
  42. def map[A](f: (Expression) ⇒ A): Seq[A]
    Definition Classes
    TreeNode
  43. def mapChildren(f: (Expression) ⇒ Expression): Expression
    Definition Classes
    TreeNode
  44. def mapProductIterator[B](f: (Any) ⇒ B)(implicit arg0: ClassTag[B]): Array[B]
    Attributes
    protected
    Definition Classes
    TreeNode
  45. val minMatchRatio: Expression
  46. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  47. def nodeName: String
    Definition Classes
    TreeNode
  48. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  49. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  50. def nullable: Boolean
    Definition Classes
    LiftOverCoordinatesExpr → Expression
  51. def numberedTreeString: String
    Definition Classes
    TreeNode
  52. val origin: Origin
    Definition Classes
    TreeNode
  53. def otherCopyArgs: Seq[AnyRef]
    Attributes
    protected
    Definition Classes
    TreeNode
  54. def p(number: Int): Expression
    Definition Classes
    TreeNode
  55. def prettyJson: String
    Definition Classes
    TreeNode
  56. def prettyName: String
    Definition Classes
    Expression
  57. def references: AttributeSet
    Definition Classes
    Expression
  58. lazy val resolved: Boolean
    Definition Classes
    Expression
  59. def semanticEquals(other: Expression): Boolean
    Definition Classes
    Expression
  60. def semanticHash(): Int
    Definition Classes
    Expression
  61. def simpleString: String
    Definition Classes
    Expression → TreeNode
  62. def sql: String
    Definition Classes
    Expression
  63. val start: Expression
  64. def stringArgs: Iterator[Any]
    Attributes
    protected
    Definition Classes
    TreeNode
  65. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  66. def toJSON: String
    Definition Classes
    TreeNode
  67. def toString(): String
    Definition Classes
    Expression → TreeNode → AnyRef → Any
  68. def transform(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  69. def transformDown(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  70. def transformUp(rule: PartialFunction[Expression, Expression]): Expression
    Definition Classes
    TreeNode
  71. def treeString(verbose: Boolean, addSuffix: Boolean): String
    Definition Classes
    TreeNode
  72. def treeString: String
    Definition Classes
    TreeNode
  73. final def verboseString: String
    Definition Classes
    Expression → TreeNode
  74. def verboseStringWithSuffix: String
    Definition Classes
    TreeNode
  75. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  76. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  77. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  78. def withNewChildren(newChildren: Seq[Expression]): Expression
    Definition Classes
    TreeNode

Inherited from Serializable

Inherited from Serializable

Inherited from ImplicitCastInputTypes

Inherited from ExpectsInputTypes

Inherited from CodegenFallback

Inherited from Expression

Inherited from TreeNode[Expression]

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped