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Merge remote-tracking branch 'remotes/origin/develop' into feature-VarscanIntoShiva
Conflicts: public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
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- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala 0 additions, 4 deletions...c/biopet/core/extensions/RscriptCommandLineFunction.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala 1 addition, 0 deletions...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala 1 addition, 0 deletions...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala 32 additions, 0 deletions...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala 126 additions, 0 deletions...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala 346 additions, 0 deletions...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 118 additions, 24 deletions.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala 2 additions, 1 deletion...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala 1 addition, 1 deletion...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala 3 additions, 3 deletions...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala 8 additions, 8 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 1 addition, 1 deletion...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala 1 addition, 1 deletion...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala 2 additions, 2 deletions...sc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
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