CNV pipeline for Exome

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

public/biopet-public-package/pom.xml

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

public/kopisu/pom.xml

...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala

...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala

public/pom.xml