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Merge branch 'feature-vcf_stats' into 'develop'
Feature vcf stats More functions can be added but this is a first version that is ready to use in the gatk pipeline. is also fix for #93 See merge request !84
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- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 7 additions, 1 deletion.../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/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/extensions/RunGubbins.scala 1 addition, 1 deletion...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala 472 additions, 0 deletions...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
- public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala 77 additions, 0 deletions...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 1 addition, 0 deletions...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
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