35 lines
1.3 KiB
Scala
35 lines
1.3 KiB
Scala
package org.broadinstitute.sting.queue.pipeline
|
|
|
|
/**
|
|
* Data validations to evaluate on a GATKReport.
|
|
*/
|
|
class PipelineTestEvalSpec {
|
|
/** List of eval modules to output. */
|
|
var evalReport: String = _
|
|
|
|
/** Validations to assert. */
|
|
var validations: List[PipelineValidation[_]] = Nil
|
|
}
|
|
|
|
/** A VariantEval JEXL and range of values to validate. */
|
|
abstract class PipelineValidation[T <: AnyVal](val table: String, val key: String, val metric: String, val target: T, val min: T, val max: T) {
|
|
def parse(x: String): T
|
|
def inRange(x: String): Boolean
|
|
}
|
|
|
|
/** A VariantEval JEXL and target to validate within a 1% tolerance. */
|
|
class IntegerValidation(table: String, key: String, metric: String, target: Int)
|
|
extends PipelineValidation[Int](table, key, metric, target,
|
|
(target * .99).floor.toInt, (target * 1.01).ceil.toInt) {
|
|
def parse(x: String) = x.toInt
|
|
def inRange(x: String) = parse(x) >= min && parse(x) <= max
|
|
}
|
|
|
|
/** A VariantEval JEXL and target to validate within a 1% tolerance. */
|
|
class DoubleValidation(table: String, key: String, metric: String, target: Double)
|
|
extends PipelineValidation(table, key, metric, target,
|
|
(target * 99).floor / 100, (target * 101).ceil / 100) {
|
|
def parse(x: String) = x.toDouble
|
|
def inRange(x: String) = parse(x) >= min && parse(x) <= max
|
|
}
|