Merge branch 'develop' into feature-FilterOnMappingQualityCarp

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala

.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala

.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala

...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala

...in/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala

...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala

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

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

...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala

.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala

...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

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

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

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