Merge branch 'develop' into feature-basty_generate_fasta

.../libraries/Maven__org_scala_lang_scala_library_2_11_2.xml

.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml

.idea/scala_compiler.xml

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

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

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

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

...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.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