Merge branch 'fix-259' into 'develop'

Fixed error message in bamutils

Fixes #259 

See merge request !311

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala

@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
   var vcfSampleList: Option[File] = config("vcf_sample_list")
   var variants: Option[Int] = config("variants")
 
+  override def defaultCoreMemory = 6.0
+
   override def beforeGraph(): Unit = {
     val validValues: Set[Int] = Set(0, 1)
     // check for boolean vars that are passed as ints

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

@@ -15,20 +15,15 @@
  */
 package nl.lumc.sasc.biopet.extensions.varscan
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetJavaCommandLineFunction }
 
-abstract class Varscan extends BiopetJavaCommandLineFunction {
+abstract class Varscan extends BiopetJavaCommandLineFunction with Version {
 
   override def subPath = "varscan" :: super.subPath
 
   jarFile = config("varscan_jar")
 
-  /**
-   * TODO: test version
-   * override def versionCommand = super.commandLine
-   * override val versionRegex = """VarScan v(.*)""".r
-   */
-
-  override def defaultCoreMemory = 5.0
+  def versionCommand = super.commandLine
+  def versionRegex = """VarScan v(.*)""".r
 }
 

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

@@ -25,7 +25,8 @@ object BamUtils {
       val inputSam = SamReaderFactory.makeDefault.open(file)
       val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
       if (samples.size == 1) samples.head -> file
-      else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+      else if (samples.size > 1) throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+      else throw new IllegalArgumentException("Bam does not contain sample ID or have no readgroups defined: " + file)
     }
     if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
     temp.toMap