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Merge from develop
Change tests to accept pindel Add testcode to accept merged VCFs
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- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala 220 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala 97 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala 95 additions, 0 deletions...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala 62 additions, 1 deletion...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
- public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala 142 additions, 0 deletions...c/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala 3 additions, 1 deletion.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala 63 additions, 0 deletions...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
- public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala 21 additions, 10 deletions...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
- public/yamsvp/.gitignore 0 additions, 1 deletionpublic/yamsvp/.gitignore
- public/yamsvp/pom.xml 0 additions, 47 deletionspublic/yamsvp/pom.xml
- public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala 0 additions, 86 deletions.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
- public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala 0 additions, 155 deletions...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
- public/yamsvp/src_old/test/resources/log4j.properties 0 additions, 25 deletionspublic/yamsvp/src_old/test/resources/log4j.properties
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