Commit bb12d6db authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed layout

parent 42ebd301
......@@ -19,8 +19,8 @@ import java.io.File
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import scala.collection.JavaConversions._
......@@ -81,10 +81,12 @@ trait Reference extends Configurable {
}
} else {
val defaults = ConfigUtils.mergeMaps(this.defaults, this.internalDefaults)
def getReferences(map: Map[String, Any]): Set[(String, String)] = (for (
(species, species_content: Map[String, Any]) <- map.getOrElse("references", Map[String, Any]()).asInstanceOf[Map[String, Any]].toList;
(reference_name, _) <- species_content.toList
) yield (species, reference_name)).toSet
val references = getReferences(defaults) ++ getReferences(Config.global.map)
if (!references.contains((referenceSpecies, referenceName))) {
val buffer = new StringBuilder()
......
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