Merge branch 'add-cnmops-kopisu' into 'develop'
Adding CNmops as method to Kopisu Depends on #369 and #370 See merge request !418
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- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala 1 addition, 1 deletion...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R 28 additions, 7 deletions...rc/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R 2 additions, 25 deletions...rces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py 126 additions, 0 deletions...ces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala 70 additions, 11 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala 3 additions, 1 deletion...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala 6 additions, 11 deletions...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala 19 additions, 0 deletions...est/scala/nl/lumc/sasc/biopet/extensions/CnmopsTest.scala
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala 15 additions, 3 deletions...n/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala 39 additions, 0 deletions...c/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala 9 additions, 1 deletion...lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala 1 addition, 0 deletions.../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala 1 addition, 0 deletions...mc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
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