Merge commit '6c473b65' into feature-merge_alleles

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

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

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

...ork/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

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

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

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...umc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

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

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala