Merge branch 'develop' into feature-vcf_stats

.idea/misc.xml

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala

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

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

...rces/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py

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

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

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

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala

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

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala