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Merge remote-tracking branch 'remotes/origin/develop' into feature-measure_modules
# Conflicts: # public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
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- public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py 49 additions, 0 deletions...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala 1 addition, 1 deletion...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala 12 additions, 0 deletions...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala 1 addition, 1 deletion...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala 14 additions, 19 deletions...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala 33 additions, 18 deletions...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala 6 additions, 1 deletion...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala 61 additions, 0 deletions...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala
- public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala 13 additions, 9 deletions...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
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