Merge branch 'develop' into feature-mergesvcalls

docs/pipelines/gears.md

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp

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

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

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

.../main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp

...c/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp

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

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

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

...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

...la/nl/lumc/sasc/biopet/core/annotations/Annotations.scala

...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

...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py