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Merge branch 'develop' into feature-Chipcap
Conflicts: public/biopet-public-package/pom.xml public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
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- .idea/misc.xml 3 additions, 0 deletions.idea/misc.xml
- public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py 0 additions, 126 deletions...rces/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala 8 additions, 1 deletion...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala 10 additions, 3 deletions...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala 34 additions, 0 deletions...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala 49 additions, 0 deletions.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala 35 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala 39 additions, 0 deletions...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala 40 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala 0 additions, 116 deletions...rc/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala 293 additions, 0 deletions.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
- public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala 230 additions, 0 deletions.../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
- public/biopet-public-package/pom.xml 5 additions, 0 deletionspublic/biopet-public-package/pom.xml
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 2 additions, 0 deletions...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala 15 additions, 10 deletions...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala 10 additions, 8 deletions...mc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
- public/kopisu/.gitignore 1 addition, 0 deletionspublic/kopisu/.gitignore
- public/kopisu/pom.xml 43 additions, 0 deletionspublic/kopisu/pom.xml
- public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala 121 additions, 0 deletions...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
- public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala 65 additions, 0 deletions...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
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