Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime

...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py

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

...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala

...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala

...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala

...c/biopet/pipelines/mapping/MultisampleMappingReport.scala

...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala

...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala