Added a precheck when using bedfiles with wrong contig in there

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -17,15 +17,16 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
+import nl.lumc.sasc.biopet.core.annotations.{AnnotationRefFlat, RibosomalRefFlat}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsCoverage, BedtoolsIntersect}
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.utils.intervals.BedCheck
 import org.broadinstitute.gatk.queue.QScript
 
 class BamMetrics(val root: Configurable) extends QScript
@@ -72,6 +73,8 @@ class BamMetrics(val root: Configurable) extends QScript
   /** executed before script */
   def init(): Unit = {
     inputFiles :+= new InputFile(inputBam)
+    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
+    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
   }
 
   /** Script to add jobs */

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala

+package nl.lumc.sasc.biopet.utils.intervals
+
+import java.io.File
+import scala.collection.mutable.Set
+
+import nl.lumc.sasc.biopet.utils.Logging
+
+/**
+  * Created by pjvanthof on 14/05/16.
+  */
+object BedCheck {
+  private val cache: Set[(File, File)] = Set()
+
+  def checkBedFileToReference(bedFile: File, reference: File, biopetError: Boolean = false, ignoreCache: Boolean = false): Unit = {
+    if (ignoreCache || !cache.contains((bedFile, reference))) {
+      cache.add((bedFile, reference))
+      val bedrecords = BedRecordList.fromFile(bedFile)
+      if (biopetError) {
+        try {
+          bedrecords.validateContigs(reference)
+        } catch {
+          case e: IllegalArgumentException => Logging.addError(e.getMessage)
+        }
+      } else bedrecords.validateContigs(reference)
+    }
+  }
+}