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Merge branch 'feature-mergesvcalls' into 'develop'
Feature mergesvcalls This branch will introduce the SV-merging tool for the VCF files generated by SV-callers in the ShivaSVcalling pipeline. We now use the PySVtools made by @wyleung closes #236 See merge request !301
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- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala 59 additions, 0 deletions...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala 35 additions, 3 deletions.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala 2 additions, 0 deletions...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala 2 additions, 0 deletions...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala 2 additions, 2 deletions...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala 2 additions, 0 deletions...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala 14 additions, 1 deletion...lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
- public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala 5 additions, 1 deletion...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
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