Merge 'develop' into 'feature-basty_generate_fasta'

biopet-framework/examples/shark_apps.json

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

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

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

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

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

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

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala

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

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

.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

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

.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala

biopet-framework/src/test/resources/paired01a.fq