Commit 54c312c0 authored by Sander Bollen's avatar Sander Bollen

set vs list

parent bcd47977
......@@ -69,17 +69,17 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
* @return
*/
def pedSamplesFromConfig(): List[PedSample] = {
val totalSampleIds = samples.values.map(_.sampleId).toList
val withFam = samples.values.filter(_.family.isDefined)
val fathers = withFam.filter(_.father.isDefined).flatMap(_.father)
val mothers = withFam.filter(_.mother.isDefined).flatMap(_.mother)
val sampleIds = withFam.map(_.sampleId).toSet
val fathers = withFam.flatMap(_.father)
val mothers = withFam.flatMap(_.mother)
fathers.foreach { f =>
if (!withFam.map(_.sampleId).toList.contains(f)) {
if (!sampleIds.contains(f)) {
Logging.addError(s"Father $f does not exist in samples")
}
}
mothers.foreach { m =>
if (!withFam.map(_.sampleId).toList.contains(m)) {
if (!sampleIds.contains(m)) {
Logging.addError(s"Mother $m does not exist in samples")
}
}
......
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