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Merge remote-tracking branch 'origin/develop' into feature-scoverage
Conflicts: protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
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- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala 1 addition, 0 deletions.../scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala 8 additions, 0 deletions...cala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala 8 additions, 0 deletions...a/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala 4 additions, 0 deletions...cala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala 1 addition, 0 deletions...st/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala 21 additions, 14 deletions...test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
- public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala 18 additions, 12 deletions...t/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala 5 additions, 1 deletion...ain/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
- public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala 1 addition, 0 deletions...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
- public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala 5 additions, 7 deletions.../lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
- public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala 4 additions, 0 deletions.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
- public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala 18 additions, 12 deletions...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala 3 additions, 0 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
- public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala 12 additions, 2 deletions.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
- public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala 2 additions, 0 deletions...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
- public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala 4 additions, 6 deletions...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
- public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala 8 additions, 2 deletions...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 3 additions, 0 deletions...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
- public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala 14 additions, 4 deletions...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
- public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala 2 additions, 0 deletions.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
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