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Merge branch 'feature-yamsvp' into 'develop'
Feature yamsvp Convert yamsvp to also work from a bam file and be included in Shiva See merge request !201
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- public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala 1 addition, 1 deletion...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala 9 additions, 13 deletions...lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala 2 additions, 2 deletions...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala 0 additions, 65 deletions.../scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala 18 additions, 20 deletions.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala 36 additions, 42 deletions...in/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala 1 addition, 0 deletions...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala 1 addition, 1 deletion.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 17 additions, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 2 additions, 1 deletion...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
- public/pom.xml 1 addition, 1 deletionpublic/pom.xml
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala 158 additions, 0 deletions.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 24 additions, 5 deletions...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
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