Merge branch 'develop' into feature-varda

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

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

...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

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

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

...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

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

...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala