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Merge branch 'develop' into feature-gentrap_additions
Conflicts: public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
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- docs/config.md 9 additions, 1 deletiondocs/config.md
- docs/general/config.md 8 additions, 1 deletiondocs/general/config.md
- docs/pipelines/bam2wig.md 17 additions, 7 deletionsdocs/pipelines/bam2wig.md
- docs/pipelines/basty.md 46 additions, 5 deletionsdocs/pipelines/basty.md
- docs/pipelines/flexiprep.md 41 additions, 19 deletionsdocs/pipelines/flexiprep.md
- docs/pipelines/gentrap.md 2 additions, 2 deletionsdocs/pipelines/gentrap.md
- docs/pipelines/mapping.md 66 additions, 26 deletionsdocs/pipelines/mapping.md
- docs/pipelines/sage.md 18 additions, 8 deletionsdocs/pipelines/sage.md
- docs/pipelines/shiva.md 66 additions, 33 deletionsdocs/pipelines/shiva.md
- docs/pipelines/toucan.md 4 additions, 3 deletionsdocs/pipelines/toucan.md
- docs/tools/VcfFilter.md 1 addition, 1 deletiondocs/tools/VcfFilter.md
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 13 additions, 3 deletions.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
- protected/biopet-gatk-pipelines/pom.xml 1 addition, 1 deletionprotected/biopet-gatk-pipelines/pom.xml
- protected/biopet-gatk-pipelines/src/test/resources/ref.dict 2 additions, 0 deletionsprotected/biopet-gatk-pipelines/src/test/resources/ref.dict
- protected/biopet-gatk-pipelines/src/test/resources/ref.fa 2 additions, 0 deletionsprotected/biopet-gatk-pipelines/src/test/resources/ref.fa
- protected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai 1 addition, 0 deletions...ected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai
- protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala 19 additions, 2 deletions.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
- protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala 17 additions, 2 deletions.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
- public/bammetrics/pom.xml 12 additions, 0 deletionspublic/bammetrics/pom.xml
- public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp 90 additions, 0 deletions...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
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