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

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

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

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

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

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

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

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

.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala

.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala

...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala

...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

...c/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

public/biopet-public-package/pom.xml

...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

public/carp/.gitignore

public/carp/pom.xml

.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

public/kopisu/.gitignore