Remove unneeded class. java and non-java jobs now both using def cmdLine

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...k/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala

...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala

...et/extensions/picard/CollectAlignmentSummaryMetrics.scala

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala

...asc/biopet/extensions/picard/CollectMultipleMetrics.scala

.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala

.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala

...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala