Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gears

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

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

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

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

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

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

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

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

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

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

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

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

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

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

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

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