Merge branch 'develop' into feature-bamToBigWig
Conflicts: public/biopet-public-package/pom.xml public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala public/pom.xml
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- docs/config.md 5 additions, 5 deletionsdocs/config.md
- protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala 8 additions, 5 deletions...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala 1 addition, 1 deletion...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala 2 additions, 2 deletions...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala 29 additions, 29 deletions...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 16 additions, 16 deletions...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 8 additions, 5 deletions.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala 0 additions, 87 deletions...umc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala 0 additions, 153 deletions...umc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala
- protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala 0 additions, 1 deletion.../nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
- public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R 0 additions, 24 deletions...esources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R
- 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/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R 35 additions, 0 deletions...rc/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
- public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R 20 additions, 0 deletions...ork/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 6 additions, 8 deletions...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 9 additions, 2 deletions...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 23 additions, 16 deletions...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 2 additions, 2 deletions.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala 8 additions, 1 deletion...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
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