Merge remote-tracking branch 'remotes/origin/develop' into feature-measure_modules

...c/biopet/core/extensions/RscriptCommandLineFunction.scala

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

...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala

...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala

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

...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

.../nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala

...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala

...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

...c/biopet/pipelines/mapping/MultisampleMappingReport.scala

...sc/biopet/pipelines/mapping/MultisampleMappingTrait.scala